[aroma.affymetrix] problems with sfit on Windows for CRMAv2 analysis

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[aroma.affymetrix] problems with sfit on Windows for CRMAv2 analysis

Johan Staaf
Hi
I am trying to run CRMAv2 analysis on some Affymetrix SNP chips, using
64-bit Windows 7. However, I continuously run into problems with the
sfit package. I installed the latest aroma.affymetrix package however
when trying:

accNormal <- AllelicCrosstalkCalibration(csNormal,model="CRMAv2")
print(accNormal)
csCNormal <- process(accNormal, verbose=verbose)

the run always end up with sfit package not loaded. However, trying to
install sfit from R-forge using the specified command from within R ends
up with saying package not available. ?

Furthermore, reading in the forum I also tried:

install.packages("sfit",repos="http://R-forge.R-project.org",
type="win.binary")

but that did not work. I also tried the 32-bit R version (latest) with
no success.

Is there a way to actually get it to work on Windows?

Best regards
Johan

--
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] problems with sfit on Windows for CRMAv2 analysis

Henrik Bengtsson-4
Hi,

thanks for reporting this.  Unfortunately, the R-forge site is lagging
behind in providing builds etc.  I'll report to them, since this is
beyond my control.  In the meanwhile, see if the following works for
you

source("http://www.braju.com/R/hbLite.R");
installPackages("http://www.braju.com/R/repos/sfit_0.1.9.zip");

then verify by running the following in a fresh R installation.

library("sfit");
example("cfit.matrix");

If it works, everything should be fine.

Also, make sure you are running R v2.12.0; that is major release when
it comes to R for Windows 64-bit!

/Henrik


On Wed, Nov 10, 2010 at 1:29 AM, Johan Staaf <[hidden email]> wrote:

> Hi
> I am trying to run CRMAv2 analysis on some Affymetrix SNP chips, using
> 64-bit Windows 7. However, I continuously run into problems with the sfit
> package. I installed the latest aroma.affymetrix package however when
> trying:
>
> accNormal <- AllelicCrosstalkCalibration(csNormal,model="CRMAv2")
> print(accNormal)
> csCNormal <- process(accNormal, verbose=verbose)
>
> the run always end up with sfit package not loaded. However, trying to
> install sfit from R-forge using the specified command from within R ends up
> with saying package not available. ?
>
> Furthermore, reading in the forum I also tried:
>
> install.packages("sfit",repos="http://R-forge.R-project.org",
> type="win.binary")
>
> but that did not work. I also tried the 32-bit R version (latest) with no
> success.
>
> Is there a way to actually get it to work on Windows?
>
> Best regards
> Johan
>
> --
> 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/
>

--
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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Re: [aroma.affymetrix] problems with sfit on Windows for CRMAv2 analysis

Johan Staaf
Hi Henrik
It worked, thanks!

Best regards
Johan
On 11/10/10 12:14 PM, Henrik Bengtsson wrote:

> Hi,
>
> thanks for reporting this.  Unfortunately, the R-forge site is lagging
> behind in providing builds etc.  I'll report to them, since this is
> beyond my control.  In the meanwhile, see if the following works for
> you
>
> source("http://www.braju.com/R/hbLite.R");
> installPackages("http://www.braju.com/R/repos/sfit_0.1.9.zip");
>
> then verify by running the following in a fresh R installation.
>
> library("sfit");
> example("cfit.matrix");
>
> If it works, everything should be fine.
>
> Also, make sure you are running R v2.12.0; that is major release when
> it comes to R for Windows 64-bit!
>
> /Henrik
>
>
> On Wed, Nov 10, 2010 at 1:29 AM, Johan Staaf<[hidden email]>  wrote:
>> Hi
>> I am trying to run CRMAv2 analysis on some Affymetrix SNP chips, using
>> 64-bit Windows 7. However, I continuously run into problems with the sfit
>> package. I installed the latest aroma.affymetrix package however when
>> trying:
>>
>> accNormal<- AllelicCrosstalkCalibration(csNormal,model="CRMAv2")
>> print(accNormal)
>> csCNormal<- process(accNormal, verbose=verbose)
>>
>> the run always end up with sfit package not loaded. However, trying to
>> install sfit from R-forge using the specified command from within R ends up
>> with saying package not available. ?
>>
>> Furthermore, reading in the forum I also tried:
>>
>> install.packages("sfit",repos="http://R-forge.R-project.org",
>> type="win.binary")
>>
>> but that did not work. I also tried the 32-bit R version (latest) with no
>> success.
>>
>> Is there a way to actually get it to work on Windows?
>>
>> Best regards
>> Johan
>>
>> --
>> 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/
>>

--
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/