[BioC] xps: returns only 21 records

[cstrato]

Dear Steve,

For your problem with 21 probesets please see:
https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-October/030258.html

Thus you need to create the scheme as follows:
scheme.mogene10stv1r4.na30 <- 
import.exon.scheme("Scheme_MoGene10stv1r4_na30_1",filedir=scmdir,
paste(libdir,"MoGene-1_0-st-v1.r4.analysis-lib-files/MoGene-1_0-st-v1.r4.clf",sep="/"),
paste(libdir,"MoGene-1_0-st-v1.r4.analysis-lib-files/MoGene-1_0-st-v1.r4.pgf",sep="/"),
paste(anndir,"MoGene-1_1-st-v1.na30.1.mm9.probeset.csv",sep="/"),
paste(anndir,"MoGene-1_1-st-v1.na30.1.mm9.transcript.csv",sep="/"))

Please note that you must download the newest 
"MoGene-1_1-st-v1.na30.1.mm9.probeset.csv" and 
"MoGene-1_1-st-v1.na30.1.mm9.transcript.csv" files from Affymetrix since 
the old files have a deleted AFFX control probeset.

Best regards
Christian


Steve Shen wrote:
> Dear Christian,
>
> Just couldn't figure out what's wrong with my practice. I have 55 
> mouse genome arrays. I tried both RMA and MAS5 for preprocession data. 
> Both methods returns only 21 readable lines. I checked the tmp_ files 
> in the folder, which seemed much bigger than just 21 lines. Any hint?
>
> Best,
> Steve
>
> > library(xps)
>
> ## import ROOT scheme and data files
> > scheme.mogene10st <- 
> root.scheme(paste(scmdir,"Scheme_MoGene10stv1r4_na30.root",sep="/"))
> > data.xps <- root.data(scheme.mogene10st, 
> paste(datdir,"gm_dk_phase2_cel.root",sep="/"))
> > data.rma.tc <http://data.rma.tc> <- rma(data.xps, 
> "tmp_gm_dk_ph2_RMA_alltc", tmpdir="", background="antigenomic", 
> normalize=TRUE, option="transcript", exonlevel="all")
>
> Creating new temporary file 
> <~/Projects/Gustavo/PhaseII/xps/tmp_gm_dk_ph2_RMA_alltc.root>...
> Opening file <~/XPS/scheme/Scheme_MoGene10stv1r4_na30.root> in <READ> 
> mode...
> Opening file <~/XPS/ROOTdata/gm_dk_phase2_cel.root> in <READ> mode...
> Added <55> trees to PreprocesSet.
> Preprocessing data using method <preprocess>...
>    Background correcting raw data...
>       setting selector mask for typepm <9276>
>       calculating background for <GM_B3_SEFCL_5.cel>...
>       background statistics:
>          1087986 cells with minimal intensity 0
>          422 cells with maximal intensity 28.291
>       calculating background for <GM_B5_SEFCL_6.cel>...
>       calculating expression for <21> of <241576> units...Finished.
>       expression statistics:
>          minimal expression level is <5.73629>
>          maximal expression level is <7406.17>
>    preprocessing finished.
> Opening file <~/XPS/scheme/Scheme_MoGene10stv1r4_na30.root> in <READ> 
> mode...
> Opening file 
> <~/Projects/Gustavo/PhaseII/xps/tmp_gm_dk_ph2_RMA_alltc.root> in 
> <READ> mode...
> Opening file 
> <~/Projects/Gustavo/PhaseII/xps/tmp_gm_dk_ph2_RMA_alltc.root> in 
> <READ> mode...
> Exporting data from tree <*> to file 
> <~/Projects/Gustavo/PhaseII/xps/tmp_gm_dk_ph2_RMA_alltc.txt>...
> Reading entries from <MoGene-1_0-st-v1.ann> ...Finished
> <21> of <21> records exported.
>
> > summary(data.rma.tc <http://data.rma.tc>)
>      Length       Class        Mode
>           1 ExprTreeSet          S4
>
> > expr.rma.tc <http://expr.rma.tc> <- validData(data.rma.tc 
> <http://data.rma.tc>)
> > dim(expr.rma.tc <http://expr.rma.tc>)
> [1] 21 55
>
> > sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base    
>
> other attached packages:
> [1] Biobase_2.6.1 xps_1.6.4   
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
>