Dear Christian, Thanks, this helps! Best, Steve On Fri, Mar 19, 2010 at 8:19 PM, cstrato <cstrato@aon.at> wrote: > Dear Steve, > > For your problem with 21 probesets please see: > > https://www.stat.math.ethz.ch/pipermail/bioconductor/2009-October/03 0258.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. >> >> > summarydata.rma.tc <http: data.rma.tc="">) >> >> Length Class Mode >> 1 ExprTreeSet S4 >> >> > expr.rma.tc <http: expr.rma.tc=""> <- validDatadata.rma.tc < >> http://data.rma.tc>) >> > dimexpr.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 >> >> > [[alternative HTML version deleted]]