[aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

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[aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

C.C.
Hello,

I was trying to run doCRMAv2.R in aroma.affymetrix 3.0 and get the error. Dose anyone know what is the problem? Thanks.



Error: The fit function for requested AvgPlm flavor failed: median

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Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

Henrik Bengtsson-2
Hi, in order for us to help you, could you please:

"[...] make sure 1) to run the latest version of the package, 2) to
report the output of sessionInfo() and traceback(), and 3) to post a
complete code example."

Thanks,

Henrik

On Thu, Mar 24, 2016 at 9:59 AM, C.C. <[hidden email]> wrote:

> Hello,
>
> I was trying to run doCRMAv2.R in aroma.affymetrix 3.0 and get the error.
> Dose anyone know what is the problem? Thanks.
>
>
>
> Error: The fit function for requested AvgPlm flavor failed: median
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [hidden email].
> For more options, visit https://groups.google.com/d/optout.

--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

C.C.
Hi Henrik,

Thanks for you email. Here is the problem I encountered.



I installed the package using, it is the latest version 3.0.0





and I was trying to run doCRMAv2

 dsList    
<- doCRMAv2(cel.subset, cdf=cdf,
 verbose
=Arguments$getVerbose(-10, timestamp=TRUE))



 and then got error information

> <simpleError: Argument 'centers' for matrixStats::rowMads() has been renamed
> to 'center'. Please update code accordingly.>
>
> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
> flavor failed: median
>
>
>
>
>   at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>
>           - getFitUnitGroupFunction.AvgPlm() is in environment
> 'aroma.affymetrix'
>
>
>
>
>   at #07. getFitUnitGroupFunction(this, ...)
>
>           - getFitUnitGroupFunction() is in environment 'aroma.affymetrix'
>
>
>
>
>   at #06. getFitUnitFunction.CnPlm(this)
>
>           - getFitUnitFunction.CnPlm() is in environment 'aroma.affymetrix'
>
>
>
>
>   at #05. getFitUnitFunction(this)
>
>           - getFitUnitFunction() is in environment 'aroma.affymetrix'
>
>
>
>
>   at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>
>           - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>
>
>
>
>   at #03. fit(plm, verbose = verbose)
>
>           - fit() is in environment 'aroma.core'
>
>
>
>
>   at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
> Arguments$getVerbose(-10,
>
>               timestamp = TRUE))
>
>           - doCRMAv2.AffymetrixCelSet() is in environment 'aroma.affymetrix'
>
>
>
>
>   at #01. doCRMAv2(cel.subset, cdf = cdf, verbose =
> Arguments$getVerbose(-10,
>
>               timestamp = TRUE))
>
>           - doCRMAv2() is in environment 'aroma.affymetrix'
>
>
>
>
> Error: The fit function for requested AvgPlm flavor failed: median
>
> 20160324 13:12:44|   Setting up parameter sets...done
>
> 20160324 13:12:44|  Fitting model of class AvgCnPlm...done
>
>>
>
 traceback()


>
> 13: stop(cond)
>
> 12: throw.Exception(Exception(...))
>
> 11: throw(Exception(...))
>
> 10: throw.default("The fit function for requested AvgPlm flavor failed: ",
>
>         flavor)
>
> 9: throw("The fit function for requested AvgPlm flavor failed: ",
>
>        flavor)
>
> 8: getFitUnitGroupFunction.AvgPlm(this, ...)
>
> 7: getFitUnitGroupFunction(this, ...)
>
> 6: getFitUnitFunction.CnPlm(this)
>
> 5: getFitUnitFunction(this)
>
> 4: fit.ProbeLevelModel(plm, verbose = verbose)
>
> 3: fit(plm, verbose = verbose)
>
> 2: doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose = v)
>
> 1: doCRMAv2(cel.subset, cdf = cdf, verbose = v)
>
>
sessionInfo()


>
> R version 3.1.0 (2014-04-10)
>
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
>
> locale:
>
>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
> LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
> LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
> LC_PAPER=en_US.iso885915
>
>  [8] LC_NAME=C                      LC_ADDRESS=C
> LC_TELEPHONE=C                 LC_MEASUREMENT=en_US.iso885915
> LC_IDENTIFICATION=C
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
> other attached packages:
>
>  [1] sfit_0.3.0              aroma.light_2.0.0       matrixStats_0.50.1
> aroma.affymetrix_2.13.1 aroma.core_2.13.0       R.devices_2.14.0
> R.filesets_2.6.0        R.utils_2.2.0           R.oo_1.20.0
> affxparser_1.36.0
>
> [11] R.methodsS3_1.7.1
>
>
> loaded via a namespace (and not attached):
>
> [1] aroma.apd_0.6.0 base64enc_0.1-4 digest_0.6.9    DNAcopy_1.38.1
> PSCBS_0.43.0    R.cache_0.12.0  R.huge_0.9.0    R.rsp_0.21.0    tools_3.1.0
>
>

On Thursday, March 24, 2016 at 12:22:36 PM UTC-7, Henrik Bengtsson wrote:
Hi, in order for us to help you, could you please:

"[...] make sure 1) to run the latest version of the package, 2) to
report the output of sessionInfo() and traceback(), and 3) to post a
complete code example."

Thanks,

Henrik

On Thu, Mar 24, 2016 at 9:59 AM, C.C. <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="oY2H6abiBAAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">chenc...@...> wrote:

> Hello,
>
> I was trying to run doCRMAv2.R in aroma.affymetrix 3.0 and get the error.
> Dose anyone know what is the problem? Thanks.
>
>
>
> Error: The fit function for requested AvgPlm flavor failed: median
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website <a href="http://www.aroma-project.org/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNGgFm4_bwjITDRdF-uORwY5SRzKjA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNGgFm4_bwjITDRdF-uORwY5SRzKjA&#39;;return true;">http://www.aroma-project.org/.
> To post to this group, send email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="oY2H6abiBAAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">aroma-af...@googlegroups.com
> To unsubscribe and other options, go to <a href="http://www.aroma-project.org/forum/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2Fforum%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNHDHkQUDcBfAJzIqTbjSXZqyWgITA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2Fforum%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNHDHkQUDcBfAJzIqTbjSXZqyWgITA&#39;;return true;">http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
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--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
 
 
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Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

Henrik Bengtsson-2
On Thu, Mar 24, 2016 at 1:54 PM, C.C. <[hidden email]> wrote:

> Hi Henrik,
>
> Thanks for you email. Here is the problem I encountered.
>
>
>
> I installed the package using, it is the latest version 3.0.0
>
>
>  source('http://callr.org/install#aroma.affymetrix')

Did you get errors and did you make sure you restarted R, because your
session information below says you're still running lots of outdated
versions, e.g. aroma.affymetrix_2.13.1.

/Henrik

>
>
>
> and I was trying to run doCRMAv2
>
>  dsList     <- doCRMAv2(cel.subset, cdf=cdf,
>  verbose=Arguments$getVerbose(-10, timestamp=TRUE))
>
>
>
>  and then got error information
>
>> <simpleError: Argument 'centers' for matrixStats::rowMads() has been
>> renamed
>> to 'center'. Please update code accordingly.>
>>
>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>> flavor failed: median
>>
>>
>>
>>
>>   at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>>
>>           - getFitUnitGroupFunction.AvgPlm() is in environment
>> 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #07. getFitUnitGroupFunction(this, ...)
>>
>>           - getFitUnitGroupFunction() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #06. getFitUnitFunction.CnPlm(this)
>>
>>           - getFitUnitFunction.CnPlm() is in environment
>> 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #05. getFitUnitFunction(this)
>>
>>           - getFitUnitFunction() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>>
>>           - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #03. fit(plm, verbose = verbose)
>>
>>           - fit() is in environment 'aroma.core'
>>
>>
>>
>>
>>   at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>> Arguments$getVerbose(-10,
>>
>>               timestamp = TRUE))
>>
>>           - doCRMAv2.AffymetrixCelSet() is in environment
>> 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #01. doCRMAv2(cel.subset, cdf = cdf, verbose =
>> Arguments$getVerbose(-10,
>>
>>               timestamp = TRUE))
>>
>>           - doCRMAv2() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>> Error: The fit function for requested AvgPlm flavor failed: median
>>
>> 20160324 13:12:44|   Setting up parameter sets...done
>>
>> 20160324 13:12:44|  Fitting model of class AvgCnPlm...done
>>
>>>
>>
>  traceback()
>
>
>>
>> 13: stop(cond)
>>
>> 12: throw.Exception(Exception(...))
>>
>> 11: throw(Exception(...))
>>
>> 10: throw.default("The fit function for requested AvgPlm flavor failed: ",
>>
>>         flavor)
>>
>> 9: throw("The fit function for requested AvgPlm flavor failed: ",
>>
>>        flavor)
>>
>> 8: getFitUnitGroupFunction.AvgPlm(this, ...)
>>
>> 7: getFitUnitGroupFunction(this, ...)
>>
>> 6: getFitUnitFunction.CnPlm(this)
>>
>> 5: getFitUnitFunction(this)
>>
>> 4: fit.ProbeLevelModel(plm, verbose = verbose)
>>
>> 3: fit(plm, verbose = verbose)
>>
>> 2: doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose = v)
>>
>> 1: doCRMAv2(cel.subset, cdf = cdf, verbose = v)
>>
>>
> sessionInfo()
>
>
>>
>> R version 3.1.0 (2014-04-10)
>>
>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>
>>
>> locale:
>>
>>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>> LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>> LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>> LC_PAPER=en_US.iso885915
>>
>>  [8] LC_NAME=C                      LC_ADDRESS=C
>> LC_TELEPHONE=C                 LC_MEASUREMENT=en_US.iso885915
>> LC_IDENTIFICATION=C
>>
>>
>> attached base packages:
>>
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>>
>> other attached packages:
>>
>>  [1] sfit_0.3.0              aroma.light_2.0.0       matrixStats_0.50.1
>> aroma.affymetrix_2.13.1 aroma.core_2.13.0       R.devices_2.14.0
>> R.filesets_2.6.0        R.utils_2.2.0           R.oo_1.20.0
>> affxparser_1.36.0
>>
>> [11] R.methodsS3_1.7.1
>>
>>
>> loaded via a namespace (and not attached):
>>
>> [1] aroma.apd_0.6.0 base64enc_0.1-4 digest_0.6.9    DNAcopy_1.38.1
>> PSCBS_0.43.0    R.cache_0.12.0  R.huge_0.9.0    R.rsp_0.21.0
>> tools_3.1.0
>>
>>
>
> On Thursday, March 24, 2016 at 12:22:36 PM UTC-7, Henrik Bengtsson wrote:
>>
>> Hi, in order for us to help you, could you please:
>>
>> "[...] make sure 1) to run the latest version of the package, 2) to
>> report the output of sessionInfo() and traceback(), and 3) to post a
>> complete code example."
>>
>> Thanks,
>>
>> Henrik
>>
>> On Thu, Mar 24, 2016 at 9:59 AM, C.C. <[hidden email]> wrote:
>> > Hello,
>> >
>> > I was trying to run doCRMAv2.R in aroma.affymetrix 3.0 and get the
>> > error.
>> > Dose anyone know what is the problem? Thanks.
>> >
>> >
>> >
>> > Error: The fit function for requested AvgPlm flavor failed: median
>> >
>> > --
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> > latest
>> > version of the package, 2) to report the output of sessionInfo() and
>> > traceback(), and 3) to post a complete code example.
>> >
>> >
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> > To post to this group, send email to [hidden email]
>> > To unsubscribe and other options, go to
>> > http://www.aroma-project.org/forum/
>> >
>> > ---
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "aroma.affymetrix" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
>> > an
>> > email to [hidden email].
>> > For more options, visit https://groups.google.com/d/optout.
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [hidden email].
> For more options, visit https://groups.google.com/d/optout.

--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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To unsubscribe and other options, go to http://www.aroma-project.org/forum/

---
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Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

Henrik Bengtsson-2
You most likely got an error during installation, because
aroma.affymetrix now requires R (≥ 3.1.2) -
https://cran.r-project.org/web/packages/aroma.affymetrix/ - and you're
on R 3.1.0, which is nearly two years old.

The solution is to update to a recent version of R, i.e. R 3.2.4.
FYI, R 3.3.0 is coming in a few weeks.

/Henrik

On Thu, Mar 24, 2016 at 2:12 PM, Henrik Bengtsson
<[hidden email]> wrote:

> On Thu, Mar 24, 2016 at 1:54 PM, C.C. <[hidden email]> wrote:
>> Hi Henrik,
>>
>> Thanks for you email. Here is the problem I encountered.
>>
>>
>>
>> I installed the package using, it is the latest version 3.0.0
>>
>>
>>  source('http://callr.org/install#aroma.affymetrix')
>
> Did you get errors and did you make sure you restarted R, because your
> session information below says you're still running lots of outdated
> versions, e.g. aroma.affymetrix_2.13.1.
>
> /Henrik
>
>>
>>
>>
>> and I was trying to run doCRMAv2
>>
>>  dsList     <- doCRMAv2(cel.subset, cdf=cdf,
>>  verbose=Arguments$getVerbose(-10, timestamp=TRUE))
>>
>>
>>
>>  and then got error information
>>
>>> <simpleError: Argument 'centers' for matrixStats::rowMads() has been
>>> renamed
>>> to 'center'. Please update code accordingly.>
>>>
>>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>>> flavor failed: median
>>>
>>>
>>>
>>>
>>>   at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>>>
>>>           - getFitUnitGroupFunction.AvgPlm() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #07. getFitUnitGroupFunction(this, ...)
>>>
>>>           - getFitUnitGroupFunction() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #06. getFitUnitFunction.CnPlm(this)
>>>
>>>           - getFitUnitFunction.CnPlm() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #05. getFitUnitFunction(this)
>>>
>>>           - getFitUnitFunction() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>>>
>>>           - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #03. fit(plm, verbose = verbose)
>>>
>>>           - fit() is in environment 'aroma.core'
>>>
>>>
>>>
>>>
>>>   at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>>> Arguments$getVerbose(-10,
>>>
>>>               timestamp = TRUE))
>>>
>>>           - doCRMAv2.AffymetrixCelSet() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #01. doCRMAv2(cel.subset, cdf = cdf, verbose =
>>> Arguments$getVerbose(-10,
>>>
>>>               timestamp = TRUE))
>>>
>>>           - doCRMAv2() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> Error: The fit function for requested AvgPlm flavor failed: median
>>>
>>> 20160324 13:12:44|   Setting up parameter sets...done
>>>
>>> 20160324 13:12:44|  Fitting model of class AvgCnPlm...done
>>>
>>>>
>>>
>>  traceback()
>>
>>
>>>
>>> 13: stop(cond)
>>>
>>> 12: throw.Exception(Exception(...))
>>>
>>> 11: throw(Exception(...))
>>>
>>> 10: throw.default("The fit function for requested AvgPlm flavor failed: ",
>>>
>>>         flavor)
>>>
>>> 9: throw("The fit function for requested AvgPlm flavor failed: ",
>>>
>>>        flavor)
>>>
>>> 8: getFitUnitGroupFunction.AvgPlm(this, ...)
>>>
>>> 7: getFitUnitGroupFunction(this, ...)
>>>
>>> 6: getFitUnitFunction.CnPlm(this)
>>>
>>> 5: getFitUnitFunction(this)
>>>
>>> 4: fit.ProbeLevelModel(plm, verbose = verbose)
>>>
>>> 3: fit(plm, verbose = verbose)
>>>
>>> 2: doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose = v)
>>>
>>> 1: doCRMAv2(cel.subset, cdf = cdf, verbose = v)
>>>
>>>
>> sessionInfo()
>>
>>
>>>
>>> R version 3.1.0 (2014-04-10)
>>>
>>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>>
>>>
>>> locale:
>>>
>>>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>>> LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>>> LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>>> LC_PAPER=en_US.iso885915
>>>
>>>  [8] LC_NAME=C                      LC_ADDRESS=C
>>> LC_TELEPHONE=C                 LC_MEASUREMENT=en_US.iso885915
>>> LC_IDENTIFICATION=C
>>>
>>>
>>> attached base packages:
>>>
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>
>>> other attached packages:
>>>
>>>  [1] sfit_0.3.0              aroma.light_2.0.0       matrixStats_0.50.1
>>> aroma.affymetrix_2.13.1 aroma.core_2.13.0       R.devices_2.14.0
>>> R.filesets_2.6.0        R.utils_2.2.0           R.oo_1.20.0
>>> affxparser_1.36.0
>>>
>>> [11] R.methodsS3_1.7.1
>>>
>>>
>>> loaded via a namespace (and not attached):
>>>
>>> [1] aroma.apd_0.6.0 base64enc_0.1-4 digest_0.6.9    DNAcopy_1.38.1
>>> PSCBS_0.43.0    R.cache_0.12.0  R.huge_0.9.0    R.rsp_0.21.0
>>> tools_3.1.0
>>>
>>>
>>
>> On Thursday, March 24, 2016 at 12:22:36 PM UTC-7, Henrik Bengtsson wrote:
>>>
>>> Hi, in order for us to help you, could you please:
>>>
>>> "[...] make sure 1) to run the latest version of the package, 2) to
>>> report the output of sessionInfo() and traceback(), and 3) to post a
>>> complete code example."
>>>
>>> Thanks,
>>>
>>> Henrik
>>>
>>> On Thu, Mar 24, 2016 at 9:59 AM, C.C. <[hidden email]> wrote:
>>> > Hello,
>>> >
>>> > I was trying to run doCRMAv2.R in aroma.affymetrix 3.0 and get the
>>> > error.
>>> > Dose anyone know what is the problem? Thanks.
>>> >
>>> >
>>> >
>>> > Error: The fit function for requested AvgPlm flavor failed: median
>>> >
>>> > --
>>> > --
>>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> > latest
>>> > version of the package, 2) to report the output of sessionInfo() and
>>> > traceback(), and 3) to post a complete code example.
>>> >
>>> >
>>> > You received this message because you are subscribed to the Google
>>> > Groups
>>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>> > To post to this group, send email to [hidden email]
>>> > To unsubscribe and other options, go to
>>> > http://www.aroma-project.org/forum/
>>> >
>>> > ---
>>> > You received this message because you are subscribed to the Google
>>> > Groups
>>> > "aroma.affymetrix" group.
>>> > To unsubscribe from this group and stop receiving emails from it, send
>>> > an
>>> > email to [hidden email].
>>> > For more options, visit https://groups.google.com/d/optout.
>>
>> --
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to [hidden email].
>> For more options, visit https://groups.google.com/d/optout.

--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

C.C.
I installed R 3.2.3 (don't know why unable to install R 3.2.4) and then reinstalled aroma.affymetrix 3.0. It worked!
Thanks Henrik!

On Thursday, March 24, 2016 at 2:16:57 PM UTC-7, Henrik Bengtsson wrote:
You most likely got an error during installation, because
aroma.affymetrix now requires R (≥ 3.1.2) -
<a href="https://cran.r-project.org/web/packages/aroma.affymetrix/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\75https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2Faroma.affymetrix%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNEsqgYYDYmn2JJKvjwHKATfG79fOw&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\75https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2Faroma.affymetrix%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNEsqgYYDYmn2JJKvjwHKATfG79fOw&#39;;return true;">https://cran.r-project.org/web/packages/aroma.affymetrix/ - and you're
on R 3.1.0, which is nearly two years old.

The solution is to update to a recent version of R, i.e. R 3.2.4.
FYI, R 3.3.0 is coming in a few weeks.

/Henrik

On Thu, Mar 24, 2016 at 2:12 PM, Henrik Bengtsson
<<a href="javascript:" target="_blank" gdf-obfuscated-mailto="dZEcVuToBAAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">henrik.b...@...> wrote:

> On Thu, Mar 24, 2016 at 1:54 PM, C.C. <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="dZEcVuToBAAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">chenc...@...> wrote:
>> Hi Henrik,
>>
>> Thanks for you email. Here is the problem I encountered.
>>
>>
>>
>> I installed the package using, it is the latest version 3.0.0
>>
>>
>>  source('<a href="http://callr.org/install#aroma.affymetrix" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fcallr.org%2Finstall%23aroma.affymetrix\46sa\75D\46sntz\0751\46usg\75AFQjCNF2izrMqwsWe6-QuS7qiy3i71osXw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fcallr.org%2Finstall%23aroma.affymetrix\46sa\75D\46sntz\0751\46usg\75AFQjCNF2izrMqwsWe6-QuS7qiy3i71osXw&#39;;return true;">http://callr.org/install#aroma.affymetrix')
>
> Did you get errors and did you make sure you restarted R, because your
> session information below says you're still running lots of outdated
> versions, e.g. aroma.affymetrix_2.13.1.
>
> /Henrik
>
>>
>>
>>
>> and I was trying to run doCRMAv2
>>
>>  dsList     <- doCRMAv2(cel.subset, cdf=cdf,
>>  verbose=Arguments$getVerbose(-10, timestamp=TRUE))
>>
>>
>>
>>  and then got error information
>>
>>> <simpleError: Argument 'centers' for matrixStats::rowMads() has been
>>> renamed
>>> to 'center'. Please update code accordingly.>
>>>
>>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>>> flavor failed: median
>>>
>>>
>>>
>>>
>>>   at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>>>
>>>           - getFitUnitGroupFunction.AvgPlm() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #07. getFitUnitGroupFunction(this, ...)
>>>
>>>           - getFitUnitGroupFunction() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #06. getFitUnitFunction.CnPlm(this)
>>>
>>>           - getFitUnitFunction.CnPlm() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #05. getFitUnitFunction(this)
>>>
>>>           - getFitUnitFunction() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>>>
>>>           - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #03. fit(plm, verbose = verbose)
>>>
>>>           - fit() is in environment 'aroma.core'
>>>
>>>
>>>
>>>
>>>   at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>>> Arguments$getVerbose(-10,
>>>
>>>               timestamp = TRUE))
>>>
>>>           - doCRMAv2.AffymetrixCelSet() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #01. doCRMAv2(cel.subset, cdf = cdf, verbose =
>>> Arguments$getVerbose(-10,
>>>
>>>               timestamp = TRUE))
>>>
>>>           - doCRMAv2() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> Error: The fit function for requested AvgPlm flavor failed: median
>>>
>>> 20160324 13:12:44|   Setting up parameter sets...done
>>>
>>> 20160324 13:12:44|  Fitting model of class AvgCnPlm...done
>>>
>>>>
>>>
>>  traceback()
>>
>>
>>>
>>> 13: stop(cond)
>>>
>>> 12: throw.Exception(Exception(...))
>>>
>>> 11: throw(Exception(...))
>>>
>>> 10: throw.default("The fit function for requested AvgPlm flavor failed: ",
>>>
>>>         flavor)
>>>
>>> 9: throw("The fit function for requested AvgPlm flavor failed: ",
>>>
>>>        flavor)
>>>
>>> 8: getFitUnitGroupFunction.AvgPlm(this, ...)
>>>
>>> 7: getFitUnitGroupFunction(this, ...)
>>>
>>> 6: getFitUnitFunction.CnPlm(this)
>>>
>>> 5: getFitUnitFunction(this)
>>>
>>> 4: fit.ProbeLevelModel(plm, verbose = verbose)
>>>
>>> 3: fit(plm, verbose = verbose)
>>>
>>> 2: doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose = v)
>>>
>>> 1: doCRMAv2(cel.subset, cdf = cdf, verbose = v)
>>>
>>>
>> sessionInfo()
>>
>>
>>>
>>> R version 3.1.0 (2014-04-10)
>>>
>>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>>
>>>
>>> locale:
>>>
>>>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>>> LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>>> LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>>> LC_PAPER=en_US.iso885915
>>>
>>>  [8] LC_NAME=C                      LC_ADDRESS=C
>>> LC_TELEPHONE=C                 LC_MEASUREMENT=en_US.iso885915
>>> LC_IDENTIFICATION=C
>>>
>>>
>>> attached base packages:
>>>
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>
>>> other attached packages:
>>>
>>>  [1] sfit_0.3.0              aroma.light_2.0.0       matrixStats_0.50.1
>>> aroma.affymetrix_2.13.1 aroma.core_2.13.0       R.devices_2.14.0
>>> R.filesets_2.6.0        R.utils_2.2.0           R.oo_1.20.0
>>> affxparser_1.36.0
>>>
>>> [11] R.methodsS3_1.7.1
>>>
>>>
>>> loaded via a namespace (and not attached):
>>>
>>> [1] aroma.apd_0.6.0 base64enc_0.1-4 digest_0.6.9    DNAcopy_1.38.1
>>> PSCBS_0.43.0    R.cache_0.12.0  R.huge_0.9.0    R.rsp_0.21.0
>>> tools_3.1.0
>>>
>>>
>>
>> On Thursday, March 24, 2016 at 12:22:36 PM UTC-7, Henrik Bengtsson wrote:
>>>
>>> Hi, in order for us to help you, could you please:
>>>
>>> "[...] make sure 1) to run the latest version of the package, 2) to
>>> report the output of sessionInfo() and traceback(), and 3) to post a
>>> complete code example."
>>>
>>> Thanks,
>>>
>>> Henrik
>>>
>>> On Thu, Mar 24, 2016 at 9:59 AM, C.C. <[hidden email]> wrote:
>>> > Hello,
>>> >
>>> > I was trying to run doCRMAv2.R in aroma.affymetrix 3.0 and get the
>>> > error.
>>> > Dose anyone know what is the problem? Thanks.
>>> >
>>> >
>>> >
>>> > Error: The fit function for requested AvgPlm flavor failed: median
>>> >
>>> > --
>>> > --
>>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> > latest
>>> > version of the package, 2) to report the output of sessionInfo() and
>>> > traceback(), and 3) to post a complete code example.
>>> >
>>> >
>>> > You received this message because you are subscribed to the Google
>>> > Groups
>>> > "aroma.affymetrix" group with website <a href="http://www.aroma-project.org/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNGgFm4_bwjITDRdF-uORwY5SRzKjA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNGgFm4_bwjITDRdF-uORwY5SRzKjA&#39;;return true;">http://www.aroma-project.org/.
>>> > To post to this group, send email to [hidden email]
>>> > To unsubscribe and other options, go to
>>> > <a href="http://www.aroma-project.org/forum/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2Fforum%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNHDHkQUDcBfAJzIqTbjSXZqyWgITA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2Fforum%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNHDHkQUDcBfAJzIqTbjSXZqyWgITA&#39;;return true;">http://www.aroma-project.org/forum/
>>> >
>>> > ---
>>> > You received this message because you are subscribed to the Google
>>> > Groups
>>> > "aroma.affymetrix" group.
>>> > To unsubscribe from this group and stop receiving emails from it, send
>>> > an
>>> > email to aroma-affymetr...@googlegroups.com.
>>> > For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;" onclick="this.href=&#39;https://groups.google.com/d/optout&#39;;return true;">https://groups.google.com/d/optout.
>>
>> --
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website <a href="http://www.aroma-project.org/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNGgFm4_bwjITDRdF-uORwY5SRzKjA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNGgFm4_bwjITDRdF-uORwY5SRzKjA&#39;;return true;">http://www.aroma-project.org/.
>> To post to this group, send email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="dZEcVuToBAAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">aroma-af...@googlegroups.com
>> To unsubscribe and other options, go to <a href="http://www.aroma-project.org/forum/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2Fforum%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNHDHkQUDcBfAJzIqTbjSXZqyWgITA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.aroma-project.org%2Fforum%2F\46sa\75D\46sntz\0751\46usg\75AFQjCNHDHkQUDcBfAJzIqTbjSXZqyWgITA&#39;;return true;">http://www.aroma-project.org/forum/
>>
>> ---
>> You received this message because you are subscribed to the Google Groups
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>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="dZEcVuToBAAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">aroma-affymetr...@googlegroups.com.
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--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
 
 
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Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

Henrik Bengtsson-2
Good to hear. /Henrik

On Fri, Mar 25, 2016 at 10:11 AM, C.C. <[hidden email]> wrote:

> I installed R 3.2.3 (don't know why unable to install R 3.2.4) and then
> reinstalled aroma.affymetrix 3.0. It worked!
> Thanks Henrik!
>
> On Thursday, March 24, 2016 at 2:16:57 PM UTC-7, Henrik Bengtsson wrote:
>>
>> You most likely got an error during installation, because
>> aroma.affymetrix now requires R (≥ 3.1.2) -
>> https://cran.r-project.org/web/packages/aroma.affymetrix/ - and you're
>> on R 3.1.0, which is nearly two years old.
>>
>> The solution is to update to a recent version of R, i.e. R 3.2.4.
>> FYI, R 3.3.0 is coming in a few weeks.
>>
>> /Henrik
>>
>> On Thu, Mar 24, 2016 at 2:12 PM, Henrik Bengtsson
>> <[hidden email]> wrote:
>> > On Thu, Mar 24, 2016 at 1:54 PM, C.C. <[hidden email]> wrote:
>> >> Hi Henrik,
>> >>
>> >> Thanks for you email. Here is the problem I encountered.
>> >>
>> >>
>> >>
>> >> I installed the package using, it is the latest version 3.0.0
>> >>
>> >>
>> >>  source('http://callr.org/install#aroma.affymetrix')
>> >
>> > Did you get errors and did you make sure you restarted R, because your
>> > session information below says you're still running lots of outdated
>> > versions, e.g. aroma.affymetrix_2.13.1.
>> >
>> > /Henrik
>> >
>> >>
>> >>
>> >>
>> >> and I was trying to run doCRMAv2
>> >>
>> >>  dsList     <- doCRMAv2(cel.subset, cdf=cdf,
>> >>  verbose=Arguments$getVerbose(-10, timestamp=TRUE))
>> >>
>> >>
>> >>
>> >>  and then got error information
>> >>
>> >>> <simpleError: Argument 'centers' for matrixStats::rowMads() has been
>> >>> renamed
>> >>> to 'center'. Please update code accordingly.>
>> >>>
>> >>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>> >>> flavor failed: median
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>> >>>
>> >>>           - getFitUnitGroupFunction.AvgPlm() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #07. getFitUnitGroupFunction(this, ...)
>> >>>
>> >>>           - getFitUnitGroupFunction() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #06. getFitUnitFunction.CnPlm(this)
>> >>>
>> >>>           - getFitUnitFunction.CnPlm() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #05. getFitUnitFunction(this)
>> >>>
>> >>>           - getFitUnitFunction() is in environment 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>> >>>
>> >>>           - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #03. fit(plm, verbose = verbose)
>> >>>
>> >>>           - fit() is in environment 'aroma.core'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>> >>> Arguments$getVerbose(-10,
>> >>>
>> >>>               timestamp = TRUE))
>> >>>
>> >>>           - doCRMAv2.AffymetrixCelSet() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #01. doCRMAv2(cel.subset, cdf = cdf, verbose =
>> >>> Arguments$getVerbose(-10,
>> >>>
>> >>>               timestamp = TRUE))
>> >>>
>> >>>           - doCRMAv2() is in environment 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>> Error: The fit function for requested AvgPlm flavor failed: median
>> >>>
>> >>> 20160324 13:12:44|   Setting up parameter sets...done
>> >>>
>> >>> 20160324 13:12:44|  Fitting model of class AvgCnPlm...done
>> >>>
>> >>>>
>> >>>
>> >>  traceback()
>> >>
>> >>
>> >>>
>> >>> 13: stop(cond)
>> >>>
>> >>> 12: throw.Exception(Exception(...))
>> >>>
>> >>> 11: throw(Exception(...))
>> >>>
>> >>> 10: throw.default("The fit function for requested AvgPlm flavor
>> >>> failed: ",
>> >>>
>> >>>         flavor)
>> >>>
>> >>> 9: throw("The fit function for requested AvgPlm flavor failed: ",
>> >>>
>> >>>        flavor)
>> >>>
>> >>> 8: getFitUnitGroupFunction.AvgPlm(this, ...)
>> >>>
>> >>> 7: getFitUnitGroupFunction(this, ...)
>> >>>
>> >>> 6: getFitUnitFunction.CnPlm(this)
>> >>>
>> >>> 5: getFitUnitFunction(this)
>> >>>
>> >>> 4: fit.ProbeLevelModel(plm, verbose = verbose)
>> >>>
>> >>> 3: fit(plm, verbose = verbose)
>> >>>
>> >>> 2: doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose = v)
>> >>>
>> >>> 1: doCRMAv2(cel.subset, cdf = cdf, verbose = v)
>> >>>
>> >>>
>> >> sessionInfo()
>> >>
>> >>
>> >>>
>> >>> R version 3.1.0 (2014-04-10)
>> >>>
>> >>> Platform: x86_64-redhat-linux-gnu (64-bit)
>> >>>
>> >>>
>> >>> locale:
>> >>>
>> >>>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>> >>> LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>> >>> LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
>> >>> LC_PAPER=en_US.iso885915
>> >>>
>> >>>  [8] LC_NAME=C                      LC_ADDRESS=C
>> >>> LC_TELEPHONE=C                 LC_MEASUREMENT=en_US.iso885915
>> >>> LC_IDENTIFICATION=C
>> >>>
>> >>>
>> >>> attached base packages:
>> >>>
>> >>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> >>>
>> >>>
>> >>> other attached packages:
>> >>>
>> >>>  [1] sfit_0.3.0              aroma.light_2.0.0
>> >>> matrixStats_0.50.1
>> >>> aroma.affymetrix_2.13.1 aroma.core_2.13.0       R.devices_2.14.0
>> >>> R.filesets_2.6.0        R.utils_2.2.0           R.oo_1.20.0
>> >>> affxparser_1.36.0
>> >>>
>> >>> [11] R.methodsS3_1.7.1
>> >>>
>> >>>
>> >>> loaded via a namespace (and not attached):
>> >>>
>> >>> [1] aroma.apd_0.6.0 base64enc_0.1-4 digest_0.6.9    DNAcopy_1.38.1
>> >>> PSCBS_0.43.0    R.cache_0.12.0  R.huge_0.9.0    R.rsp_0.21.0
>> >>> tools_3.1.0
>> >>>
>> >>>
>> >>
>> >> On Thursday, March 24, 2016 at 12:22:36 PM UTC-7, Henrik Bengtsson
>> >> wrote:
>> >>>
>> >>> Hi, in order for us to help you, could you please:
>> >>>
>> >>> "[...] make sure 1) to run the latest version of the package, 2) to
>> >>> report the output of sessionInfo() and traceback(), and 3) to post a
>> >>> complete code example."
>> >>>
>> >>> Thanks,
>> >>>
>> >>> Henrik
>> >>>
>> >>> On Thu, Mar 24, 2016 at 9:59 AM, C.C. <[hidden email]> wrote:
>> >>> > Hello,
>> >>> >
>> >>> > I was trying to run doCRMAv2.R in aroma.affymetrix 3.0 and get the
>> >>> > error.
>> >>> > Dose anyone know what is the problem? Thanks.
>> >>> >
>> >>> >
>> >>> >
>> >>> > Error: The fit function for requested AvgPlm flavor failed: median
>> >>> >
>> >>> > --
>> >>> > --
>> >>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >>> > latest
>> >>> > version of the package, 2) to report the output of sessionInfo() and
>> >>> > traceback(), and 3) to post a complete code example.
>> >>> >
>> >>> >
>> >>> > You received this message because you are subscribed to the Google
>> >>> > Groups
>> >>> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> >>> > To post to this group, send email to [hidden email]
>> >>> > To unsubscribe and other options, go to
>> >>> > http://www.aroma-project.org/forum/
>> >>> >
>> >>> > ---
>> >>> > You received this message because you are subscribed to the Google
>> >>> > Groups
>> >>> > "aroma.affymetrix" group.
>> >>> > To unsubscribe from this group and stop receiving emails from it,
>> >>> > send
>> >>> > an
>> >>> > email to [hidden email].
>> >>> > For more options, visit https://groups.google.com/d/optout.
>> >>
>> >> --
>> >> --
>> >> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> latest
>> >> version of the package, 2) to report the output of sessionInfo() and
>> >> traceback(), and 3) to post a complete code example.
>> >>
>> >>
>> >> You received this message because you are subscribed to the Google
>> >> Groups
>> >> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> >> To post to this group, send email to [hidden email]
>> >> To unsubscribe and other options, go to
>> >> http://www.aroma-project.org/forum/
>> >>
>> >> ---
>> >> You received this message because you are subscribed to the Google
>> >> Groups
>> >> "aroma.affymetrix" group.
>> >> To unsubscribe from this group and stop receiving emails from it, send
>> >> an
>> >> email to [hidden email].
>> >> For more options, visit https://groups.google.com/d/optout.
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
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> For more options, visit https://groups.google.com/d/optout.

--
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


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