[BioC] error using frma() with brainarray CDFs

Ty Thomson tthomson at selventa.com
Thu May 2 17:04:36 CEST 2013 

Hi Matt,

Thanks, I upgraded to hgu133afrmavecs_1.2.0 and everything appears to be working!

Ty

-----Original Message-----
From: Matthew McCall [mailto:mccallm at gmail.com] 
Sent: Thursday, May 02, 2013 10:59 AM
To: Ty Thomson
Cc: bioconductor at r-project.org
Subject: Re: [BioC] error using frma() with brainarray CDFs

Upgrading to hgu133afrmavecs_1.2.0 or downgrading to
hgu133ahsentrezgcdf_15.0.0 should solve your problem. The Brain Array version release schedule not matching the BioC release schedule is what causes this headache. Sorry.

Best,
Matt





On Thu, May 2, 2013 at 10:49 AM, Ty Thomson <tthomson at selventa.com> wrote:
> Hi Matt,
>
> Apologies, here's sessionInfo():
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] hgu133afrmavecs_1.1.13     frma_1.10.0                hgu133ahsentrezgcdf_16.0.0 AnnotationDbi_1.20.7
> [5] frmaExampleData_0.99.4     BiocInstaller_1.8.3        affy_1.36.1                Biobase_2.18.0
> [9] BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.30.2     affyio_1.26.0         Biostrings_2.26.3     bit_1.1-10            codetools_0.2-8
>  [6] DBI_0.2-6             ff_2.2-11             foreach_1.4.0         GenomicRanges_1.10.7  IRanges_1.16.6
> [11] iterators_1.0.6       MASS_7.3-23           oligo_1.22.0          oligoClasses_1.20.0   parallel_2.15.2
> [16] preprocessCore_1.20.0 RSQLite_0.11.3        splines_2.15.2        stats4_2.15.2         tools_2.15.2
> [21] zlibbioc_1.4.0
>
>
> So I guess I'm using v16 of the brainarray CDFs and v 1.1.13 of frmavecs.
>
> Thanks!
>
> Ty
>
> -----Original Message-----
> From: Matthew McCall [mailto:mccallm at gmail.com]
> Sent: Thursday, May 02, 2013 10:42 AM
> To: Ty Thomson
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] error using frma() with brainarray CDFs
>
> Ty,
>
> Can you send your sessionInfo after loading the frma and frmavecs packages? I tried to reproduce your error and wasn't able to -- this might mean you have an old version of frma or the hgu133afrmavecs package. Or it could be that your Brain Array CDF doesn't match the current frmavecs alternative CDF -- which version of the Brain Array Entrez Gene CDF are you using?
>
> Best,
> Matt
>
>
>
> On Thu, May 2, 2013 at 10:28 AM, Ty Thomson <tthomson at selventa.com> wrote:
>> Hi Group,
>>
>> When I try to run frma() using brainarray cdfs I get an error (the chips are HG-U133A):
>>
>>> affy.batch <- ReadAffy(cdfname="hgu133ahsentrezg")
>>> eset.frma <- frma(affy.batch)
>> Error in rcModelWPLM(y = x1, w = w.tmp, row.effects = pe.tmp, input.scale = x4) :
>>   row.effects should sum to zero
>>
>>
>> I can run frma() without specifying a custom CDF, and rma() with the brainarray CDF, which suggest to me that the problem isn't with the data, frma(), or the brainarray CDF itself.  When I try "median_polish" or "weighted_average" options for summarize I get an ominous warning instead of an error:
>>
>>> eset.frma <- frma(affy.batch, summarize="median_polish")
>> Warning message:
>> In log2(pms) - input.vecs$probeVec :
>>   longer object length is not a multiple of shorter object length
>>
>>
>> I get similar errors/warnings when I use 'AffyBatchExample' from 'frmaExampleData':
>>
>>> library(frmaExampleData)
>>> data(AffyBatchExample)
>>> AffyBatchExample at cdfName
>> [1] "HG-U133A"
>>> affy.batch <- AffyBatchExample
>>> affy.batch at cdfName <- "hgu133ahsentrezg"
>>> eset.frma <- frma(affy.batch, summarize="median_polish")
>> Warning message:
>> In log2(pms) - input.vecs$probeVec :
>>   longer object length is not a multiple of shorter object length
>>
>>
>> One thing to note is that I'm running R2.15.2 and when 'AnnotationDbi' is loaded a warning is generated:
>>
>> Warning message:
>> package 'AnnotationDbi' was built under R version 2.15.3
>>
>>
>> I would update to R 2.15.3 but naively I don't know if this will cause problems with any other packages that I've installed.
>>
>> Here is my sessionInfo:
>>
>>> sessionInfo()
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] affy_1.36.1        Biobase_2.18.0     BiocGenerics_0.4.0
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.26.0         BiocInstaller_1.8.3   preprocessCore_1.20.0 tools_2.15.2          zlibbioc_1.4.0
>>
>>
>> Any suggestions/help would be much appreciated!
>>
>> Ty M. Thomson, Ph.D.
>> Senior Computational Biologist
>> Selventa
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
> --
> Matthew N McCall, PhD
> 112 Arvine Heights
> Rochester, NY 14611
> Cell: 202-222-5880
>
>



--
Matthew N McCall, PhD
112 Arvine Heights
Rochester, NY 14611
Cell: 202-222-5880

More information about the Bioconductor mailing list