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

[Zhu, Jack (NIH/NCI) [C]]

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