[BioC] using frma and brainarray cdf on exon arrays

[Ty Thomson]

Hi Matt,

Thanks for the quick reply and the suggestions.  I'll look into making my own pd annotation and frmavecs packages.

Ty


-----Original Message-----
From: Matthew McCall [mailto:mccallm at gmail.com] 
Sent: Monday, January 13, 2014 3:14 PM
To: Ty Thomson
Cc: bioconductor at r-project.org
Subject: Re: using frma and brainarray cdf on exon arrays

Ty,

Unfortunately, what you are attempting to do is not currently implemented. The frmavecs packages for the 3' Affy arrays (HGU133a, HGU133plus2, etc) contain implementations for both the Affy and BrainArray CDFs. The issue is with the newer Affy arrays (HuGene 1.0 ST, etc.), which should really be read in using the oligo package and corresponding pd annotation packages. This is implemented in frma for the Affy annotation, but currently the BrainArray folks provide CDFs, which can't be readily used. This may be changing fairly soon -- I believe the BrainArray group may start offering oligo compatible annotation packages. Until then, to do what you would like would
require: (1) making your own pd annotation package corresponding to the BrainArray alternative CDF, and (2) creating your own frmavecs package for the alternative annotation.

Best,
Matt


On Mon, Jan 13, 2014 at 2:53 PM, Ty Thomson <tthomson at selventa.com> wrote:
> Apologies if any of my questions are naïve, as I don't have a lot of 
> experience with exon arrays.  I would like to analyze an Affy HuGene 
> 1.0 ST array using the brainArray CDF (because I want to get 
> expression values on a per gene level), and use fRMA (to correct for 
> batch effects and enable me to add additional samples in the future 
> without redoing RMA).  Is this possible?  Here's what I've tried without much success thus far:
>
>
>
> I can skip brainarray and just load the data and run fRMA without error:
>
>> exonFS <- read.celfiles(filenames=cel.files, verbose=F, 
>> celfile.path=NULL)
>
>> tmp.eset <- frma(exonFS, summarize="median_polish")
>
>
>
> But when I use ReadAffy and specify the cdf, fRMA generates an error:
>
>> Affybatch <- ReadAffy(filenames=cel.files, verbose=F, 
>> celfile.path=NULL,
>> cdfname="hugene10sthsentrezg")
>
> Warning message:
>
>
>
> The affy package can process data from the Gene ST 1.x series of 
> arrays,
>
> but you should consider using either the oligo or xps packages, which 
> are specifically
>
> designed for these arrays.
>
>
>
>> tmp.eset <- frma(Affybatch, summarize="median_polish")
>
> Error in frmaMedPol(object, background, normalize, target, input.vecs,  :
>
>   hugene10stfrmavecs package must be installed first
>
> In addition: Warning message:
>
> In library(package, lib.loc = lib.loc, character.only = TRUE, 
> logical.return = TRUE,  :
>
>   there is no package called 'hugene10stfrmavecs'
>
>
>
>
>
> When I try running fRMA while directly passing the frmavecs to the 
> function I get a different error:
>
>> data(hugene.1.0.st.v1frmavecs)
>
>> tmp.eset <- frma(Affybatch, summarize="median_polish",
>> input.vecs=hugene.1.0.st.v1frmavecs)
>
> Warning message:
>
> In log2(pms) - input.vecs$probeVec :
>
>   longer object length is not a multiple of shorter object length
>
>
>
>
>
> Thanks in advance for any help,
>
>
>
> Ty
>
>
>
>
>
>> sessionInfo()
>
> R version 3.0.1 (2013-05-16)
>
> 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] parallel  stats     graphics  grDevices utils     datasets  methods
> base
>
>
>
> other attached packages:
>
> [1] hugene10sthsentrezgcdf_17.1.0  AnnotationDbi_1.22.6
> hugene.1.0.st.v1frmavecs_0.0.3 pd.hugene.1.0.st.v1_3.8.0
>
>  [5] RSQLite_0.11.4                 DBI_0.2-7
> frma_1.12.0                    oligo_1.24.2
>
>  [9] oligoClasses_1.22.0            affy_1.38.1
> Biobase_2.20.1                 BiocGenerics_0.6.0
>
>
>
> loaded via a namespace (and not attached):
>
> [1] affxparser_1.32.3     affyio_1.28.0         BiocInstaller_1.10.4
> Biostrings_2.28.0     bit_1.1-11            codetools_0.2-8
>
>  [7] ff_2.2-12             foreach_1.4.1         GenomicRanges_1.12.5
> IRanges_1.18.4        iterators_1.0.6       MASS_7.3-29
>
> [13] preprocessCore_1.22.0 splines_3.0.1         stats4_3.0.1
> tools_3.0.1           zlibbioc_1.6.0



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