[BioC] Problem with rma function in xps package with Affymetrix Human Gene 1.0 ST Array

[cstrato]

Dear Jack,

Please note that with release r4 Affymetrix has converted HuGene to an 
exon array, thus you need either to use the old r3 CLF/PGF files or use 
"import.exon.scheme". For more details please see:
https://stat.ethz.ch/pipermail/bioconductor/2009-February/026360.html
https://stat.ethz.ch/pipermail/bioconductor/2009-February/026472.html

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._


Zhu, Jack (NIH/NCI) [C] wrote:
> Dear list,
>
> Recently I tried to use xps package to process Affymetrix Human Gene 1.0 ST
> Array data. It seems that all low level analysis is fine.  But there are
> always problems with rma function from my many tires, specifically, rma
> always gives me expression data of  57 genes (?). Also I don't see Affy
> probeset names in the rma output.
>
> Please see my codes below:
>
>   
>> scheme <- import.genome.scheme("Scheme_HuGene10stv1r4_na28",filedir=scmdir,
>>     
> paste(libdir,"HuGene-1_0-st-v1.r4.clf",sep="/"),
> paste(libdir,"HuGene-1_0-st-v1.r4.pgf",sep="/"),
> paste(anndir,"HuGene-1_0-st-v1.na28.hg18.transcript.csv",sep="/"))
>   
> Creating new file 
> </Applications/xps/scheme/Scheme_HuGene10stv1r4_na28.root>...
> Importing </Applications/xps/library/HuGene-1_0-st-v1.r4.clf> as
> <HuGene-1_0-st-v1.cxy>...
>    <1102500> records imported...Finished
> New dataset <HuGene-1_0-st-v1> is added to Content...
> Importing 
> </Applications/xps/annotation/HuGene-1_0-st-v1.na28.hg18.transcript.csv> as
> <HuGene-1_0-st-v1.ann>...
>    Number of transcripts is <33297>.
>    <861493> records imported...Finished
>    <257430> total transcript units imported.
>    Genome cell statistics:
>       Number of unit cells: minimum = 1,  maximum = 1189
> Finishedsetwd('/Users/zhujack/Documents/Work/Projects/dan/Affy')
>
>
>   
>> data <- import.data( scheme, "Dan_affy", celdir = celdir, celfiles = celfiles)
>>     
>
> Opening file </Applications/xps/scheme/Scheme_HuGene10stv1r4_na28.root> in
> <READ> mode...
> Creating new file 
> </Users/zhujack/Documents/Work/Projects/dan/Affy/Dan_affy_cel.root>...
> Importing <./CMPC_WT_Test_run.CEL> as <CMPC_WT_Test_run.cel>...
>    <1102500> records imported...
>    hybridization statistics:
>       2 cells with minimal intensity 32
>       2 cells with maximal intensity 65534
> New dataset <DataSet> is added to Content...
> Importing <./CMPC_WT_Test_run2.CEL> as <CMPC_WT_Test_run2.cel>...
>    <40001> records imported...
>
>   
>> data.rma <- rma(data,"Dan_Affy_RMA", ,tmpdir="", background="antigenomic",
>>     
> normalize=T, exonlevel="metacore+affx")
>
> Creating new file 
> </Users/zhujack/Documents/Work/Projects/dan/Affy/Dan_Affy_RMA.root>...
> Opening file </Applications/xps/scheme/Scheme_HuGene10stv1r4_na28.root> in
> <READ> mode...
> Opening file 
> </Users/zhujack/Documents/Work/Projects/dan/Affy/Dan_affy_cel.root> in
> <READ> mode...
> Preprocessing data using method <preprocess>...
>    Background correcting raw data...
>       setting selector mask for typepm <8252>
>       calculating background for <CMPC_WT_Test_run.cel>...
>       background statistics:
>          1097995 cells with minimal intensity 0
>          6 cells with maximal intensity 60.8093
>       calculating background for <CMPC_WT_Test_run2.cel>...
>       calculating expression for <57> of <257430> units...Finished.
>       expression statistics:
>          minimal expression level is <3.52152>
>          maximal expression level is <6634.65>
>    preprocessing finished.
> Opening file </Applications/xps/scheme/Scheme_HuGene10stv1r4_na28.root> in
> <READ> mode...
> Opening file 
> </Users/zhujack/Documents/Work/Projects/dan/Affy/Dan_Affy_RMA.root> in
> <READ> mode...
> Opening file 
> </Users/zhujack/Documents/Work/Projects/dan/Affy/Dan_Affy_RMA.root> in
> <READ> mode...
> Exporting data from tree <*> to file
> </Users/zhujack/Documents/Work/Projects/dan/Affy/Dan_Affy_RMA.txt>...
> Reading entries from <HuGene-1_0-st-v1.ann> ...Finished
> <57> of <57> records exported.
>
> ----------
> Your help will be greatly appreciated.
>
> Jack
> --
> Yuelin Jack Zhu
>
> Genetics Branch/CCR/NCI/NIH
> Tel: (301)496-4527
> FAX: (301) 402-3241
> E-mail: zhujack at mail.nih.gov
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>