[BioC] Using fRMA with "alternative" CDF files

[Matthew McCall]

Adam,

The entrez gene alternative cdf is supported for the mouse4302 array,
so it should work.

Can you send me the commands you ran? Something like:
obj <- ReadAffy()
eset <- frma(obj)

Best,
Matt

On Thu, Jan 3, 2013 at 4:30 PM, Cornwell, Adam
<Adam_Cornwell at urmc.rochester.edu> wrote:
> Hello,
>
> I'm trying to using fRMA on a set of human u133+ 2.0 arrays and a set of mouse 430 2.0 arrays. Lately I've been using the BrainArray Entrezgene-derived CDFs in normalization. With the human dataset, I have no issues using the alternative CDF with fRMA, but with the mouse 430 2.0 arrays I get
> "Error in solve.default(xtx, xty) :
>   system is computationally singular: reciprocal condition number = 0"
> When I use the default CDF (by not specifying a CDF when loading in with ReadAffy()) fRMA works fine, so it seems like the issue is with the fRMA and the alternative CDF. Is use of the alternative CDFs supported with fRMA?
>
> Thanks!
> Adam Cornwell
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-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] mouse4302cdf_2.11.0          mouse4302frmavecs_1.1.12     mouse4302mmentrezgcdf_16.0.0 AnnotationDbi_1.20.2
> [5] affy_1.36.0                  frma_1.10.0                  Biobase_2.18.0               BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.30.0     affyio_1.26.0         BiocInstaller_1.8.3   Biostrings_2.26.2     bit_1.1-9             codetools_0.2-8
>  [7] DBI_0.2-5             ff_2.2-10             foreach_1.4.0         GenomicRanges_1.10.3  IRanges_1.16.3        iterators_1.0.6
> [13] MASS_7.3-22           oligo_1.22.0          oligoClasses_1.20.0   parallel_2.15.1       preprocessCore_1.20.0 RSQLite_0.11.2
> [19] splines_2.15.1        stats4_2.15.1         tools_2.15.1          zlibbioc_1.4.0
>
>         [[alternative HTML version deleted]]
>
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Matthew N McCall, PhD
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