[BioC] error using frma() with brainarray CDFs

[Ty Thomson]

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]]
>
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