Re: [aroma.affymetrix] Error using RMA

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Re: [aroma.affymetrix] Error using RMA

Pabita Saud
Hi,
I followed the aroma project to create a custom cdf package. I succeed in doing that. Now I want to see the expression of genes from  a .cel file with my cdf package in compare to that with previous cdf. When I tried to use normalization (rma) to the affy object (with previous cdf), I can get expression set,

>rawdata<-ReadAffy("GSM1090980_ZE010001.CEL",cdfname ="syng007a520046cdf" )

>rawdata
AffyBatch object
size of arrays=1164x1164 features (17 kb)
cdf=syng007a520046cdf (82661 affyids)
number of samples=1
number of genes=82661
annotation=syng007a520046cdf
notes=

>rma(rawdata)
Background correcting
Normalizing
Calculating Expression
ExpressionSet (storageMode: lockedEnvironment)
assayData: 82661 features, 1 samples 
  element names: exprs 
protocolData
  sampleNames: GSM1090980_ZE010001.CEL
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: GSM1090980_ZE010001.CEL
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: syng007a520046cdf 

But, if same process is applied to my cdf, I get an error,
>rawdata_mycdf<-ReadAffy("GSM1090980_ZE010001.CEL",cdfname ="gpl16720syng007a520046.mycdf")
>rawdata_mycdf
AffyBatch object
size of arrays=1164x1164 features (17 kb)
cdf=gpl16720syng007a520046.mycdf (8858 affyids)
number of samples=1
number of genes=8858
annotation=gpl16720syng007a520046.mycdf
notes=

>rma(rawdata_mycdf)
Error in exprs(object)[index, , drop = FALSE] : subscript out of bounds

I will really appreciate your help.
Thank you.

Best Regards,
Pabita

Best Regards,
Pabita

On Tue, Dec 19, 2017 at 12:38 PM, Karyn Meltz Steinberg <[hidden email]> wrote:
Thank you so much--Number 1 was indeed the issue. I truly appreciate your quick response.

Best,
KMS

On Monday, December 18, 2017 at 10:49:06 PM UTC-6, Henrik Bengtsson wrote:
Hi.  From your verbose output, I think two things can have happened:

1. This error happens when it tries to write to the file cache, which
is located under ~/.Rcache/.  It could be that this cache is using up
your home drive/folder/account.  Not sure what OS you're on, but to
find where `~` is use `normalizePath("~").   If that is indeed full,
and you're on Unix/macOS, the easiest is to simply point `~/.Rcache/`
to another drive via symbol links, e.g. `mkdir -p /scratch/$USER; mv
~/.Rcache /scratch/$USER/; ln -s /scratch/$USER/ ~/.Rcache`.

2. Alternatively, it could just be a hiccup on your system, which
means you can just rerun the script (it should quickly skip everything
already processed in previous runs).

I think (1) is the most likely reason, because the error is in
`base_save(file = fh, object, compress = compress, ...)` which happens
after two very similar calls to the same file which did _not_ fail,
cf. https://github.com/HenrikBengtsson/R.cache/blob/0.12.0/R/saveCache.R#L111.
(I'll see if I can add a more informative error message in a future
version of R.cache, e.g. including the problematic filename.)

Hope this helps

Henrik

On Mon, Dec 18, 2017 at 3:25 PM, Karyn Meltz Steinberg
<[hidden email]> wrote:

> Hello,
>
> I am running doCRMAv2 on 8 CytoScanHD .CEL files. I get the following error
> in the  CRMAv2/Export to technology-independent data files...
> step:
>
> Error in base_save(file = fh, object, compress = compress, ...) :
>   error writing to connection
> In addition: Warning message:
> In readRDS(con) : error reading from connection
>           Saving to file cache...done
>          Getting (unit, group, cell) map...done
>         Extracting (total, freqB)...done
>        Reading data...done
>       Exporting CnChipEffectFile as an AromaUnitTotalCnBinaryFile...done
>      Exporting (total, fracB) data...done
>     Array #1 ('GBD-035') of 8...done
>    Exporting CnChipEffectSet as AromaUnitTotalCnBinarySet...done
>
> I have enough space on the disk and the correct permissions. I am running
> version 3.1.0 on R3.4.0. Any advice would be greatly appreciated
>
> Best,
> Karyn
>
> --
> --
> 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
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> To post to this group, send email to [hidden email]
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>
> ---
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--
--
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Re: [aroma.affymetrix] Error using RMA

Henrik Bengtsson-2
Hi,

so that example code uses the affy package of Bioconductor and not the
aroma.affymetrix framework.  It might be that there is a bug in the
affy package or that it does not support custom CDFs well enough.  It
could also be that the chip type you're using is special and not well
suited from customization.

I would recommend you to make sure your custom CDF first using the
doRMA() function in aroma.affymetrix.

/Henrik

PS. Please do not hijack old email threads; instead start with a new
message whenever you have a new topic.


On Fri, Dec 22, 2017 at 8:32 AM, Pabita Saud <[hidden email]> wrote:

> Hi,
> I followed the aroma project to create a custom cdf package. I succeed in
> doing that. Now I want to see the expression of genes from  a .cel file with
> my cdf package in compare to that with previous cdf. When I tried to use
> normalization (rma) to the affy object (with previous cdf), I can get
> expression set,
>
>>rawdata<-ReadAffy("GSM1090980_ZE010001.CEL",cdfname ="syng007a520046cdf" )
>
>>rawdata
> AffyBatch object
> size of arrays=1164x1164 features (17 kb)
> cdf=syng007a520046cdf (82661 affyids)
> number of samples=1
> number of genes=82661
> annotation=syng007a520046cdf
> notes=
>
>>rma(rawdata)
> Background correcting
> Normalizing
> Calculating Expression
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 82661 features, 1 samples
>   element names: exprs
> protocolData
>   sampleNames: GSM1090980_ZE010001.CEL
>   varLabels: ScanDate
>   varMetadata: labelDescription
> phenoData
>   sampleNames: GSM1090980_ZE010001.CEL
>   varLabels: sample
>   varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation: syng007a520046cdf
>
> But, if same process is applied to my cdf, I get an error,
>>rawdata_mycdf<-ReadAffy("GSM1090980_ZE010001.CEL",cdfname
>> ="gpl16720syng007a520046.mycdf")
>>rawdata_mycdf
> AffyBatch object
> size of arrays=1164x1164 features (17 kb)
> cdf=gpl16720syng007a520046.mycdf (8858 affyids)
> number of samples=1
> number of genes=8858
> annotation=gpl16720syng007a520046.mycdf
> notes=
>
>>rma(rawdata_mycdf)
> Error in exprs(object)[index, , drop = FALSE] : subscript out of bounds
>
> I will really appreciate your help.
> Thank you.
>
> Best Regards,
> Pabita
>
> Best Regards,
> Pabita

[...]

> --
> --
> 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/

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Re: [aroma.affymetrix] Error using RMA

Pabita Saud
Thank you.

Best Regards,
Pabita

On Fri, Dec 22, 2017 at 12:02 PM, Henrik Bengtsson <[hidden email]> wrote:
Hi,

so that example code uses the affy package of Bioconductor and not the
aroma.affymetrix framework.  It might be that there is a bug in the
affy package or that it does not support custom CDFs well enough.  It
could also be that the chip type you're using is special and not well
suited from customization.

I would recommend you to make sure your custom CDF first using the
doRMA() function in aroma.affymetrix.

/Henrik

PS. Please do not hijack old email threads; instead start with a new
message whenever you have a new topic.


On Fri, Dec 22, 2017 at 8:32 AM, Pabita Saud <[hidden email]> wrote:
> Hi,
> I followed the aroma project to create a custom cdf package. I succeed in
> doing that. Now I want to see the expression of genes from  a .cel file with
> my cdf package in compare to that with previous cdf. When I tried to use
> normalization (rma) to the affy object (with previous cdf), I can get
> expression set,
>
>>rawdata<-ReadAffy("GSM1090980_ZE010001.CEL",cdfname ="syng007a520046cdf" )
>
>>rawdata
> AffyBatch object
> size of arrays=1164x1164 features (17 kb)
> cdf=syng007a520046cdf (82661 affyids)
> number of samples=1
> number of genes=82661
> annotation=syng007a520046cdf
> notes=
>
>>rma(rawdata)
> Background correcting
> Normalizing
> Calculating Expression
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 82661 features, 1 samples
>   element names: exprs
> protocolData
>   sampleNames: GSM1090980_ZE010001.CEL
>   varLabels: ScanDate
>   varMetadata: labelDescription
> phenoData
>   sampleNames: GSM1090980_ZE010001.CEL
>   varLabels: sample
>   varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation: syng007a520046cdf
>
> But, if same process is applied to my cdf, I get an error,
>>rawdata_mycdf<-ReadAffy("GSM1090980_ZE010001.CEL",cdfname
>> ="gpl16720syng007a520046.mycdf")
>>rawdata_mycdf
> AffyBatch object
> size of arrays=1164x1164 features (17 kb)
> cdf=gpl16720syng007a520046.mycdf (8858 affyids)
> number of samples=1
> number of genes=8858
> annotation=gpl16720syng007a520046.mycdf
> notes=
>
>>rma(rawdata_mycdf)
> Error in exprs(object)[index, , drop = FALSE] : subscript out of bounds
>
> I will really appreciate your help.
> Thank you.
>
> Best Regards,
> Pabita
>
> Best Regards,
> Pabita

[...]

> --
> --
> 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/

---
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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.
 
 
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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