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/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
>>
>>
>

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