Hello Christian,
Thank you very much for you help. It works fine.
Michael
> -----Urspr?ngliche Nachricht-----
> Von: "cstrato" <cstrato at="" aon.at="">
> Gesendet: 19.05.09 21:53:32
> An: Michael Walter <michael.walter at="" med.uni-tuebingen.de="">
> CC: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] xps - number of probesets for HuGene10ST array
> Dear Michael
>
> If you really want to compute unmapped FLmRNAs and pos/neg controls
> together with "core+affx" probesets, you can do:
>
> data.rma <- rma(data.genome, "HuGeneMixRMA926780", filedir=datdir,
> tmpdir="", background="antigenomic", normalize=T,
> exonlevel=c(926780,926780,926780))
> export.expr(data.rma, outfile="HuGeneMixRMA926780.txt")
>
> Until now this was an undocumented feature since I do not recommend
to
> use these probesets, because in my opinion they will only add noise
to
> the "core" probesets. However, in the new version "xps_1.4.3" I have
> updated the help "?exonLevel", which shows you which numbers to add
for
> the different combinations.
>
> In principle, it is now also possible to use all 33297 probesets,
> including the antigenomic probesets by setting
> "exonlevel=c(992316,992316,992316)". However, in this case you need
to
> update to "xps_1.4.3", otherwise you will get a bus error.
>
> Best regards
> Christian
>
>
> Michael Walter wrote:
> > Dear Christian,
> >
> > Thanks for your reply. That makes things clear. I was missing the
unmapped FLmRNAs. However, is there a way to get also the summarized
signals for the control probes? Affy is recommending ROCs between
positive and negative controls for QC and I'd like to calculate this
directly in Bioconductor.
> >
> > Thanks again,
> >
> > Michael
> >
> >
> >> -----Urspr?ngliche Nachricht-----
> >> Von: "cstrato" <cstrato at="" aon.at="">
> >> Gesendet: 15.05.09 20:57:05
> >> An: Michael Walter <michael.walter at="" med.uni-tuebingen.de="">
> >> CC: bioconductor at stat.math.ethz.ch
> >> Betreff: Re: [BioC] xps - number of probesets for HuGene10ST
array
> >>
> >
> >
> >
> >> Dear Michael
> >>
> >> When you look at the annotation file
> >> "HuGene-1_0-st-v1.na27.hg18.transcript.csv" you will see that it
> >> contains in total 33297 probesets, which are divided as follows:
> >>
> >> 28869 "main"
> >> 57 "control->affx"
> >> 45 "control->bgp->antigenomic"
> >> 1195 "normgene->exon"
> >> 2904 "normgene->intron"
> >> 227 "rescue->FLmRNA->unmapped"
> >>
> >> For further analysis, e.g. rma, only "main" and "affx" are used
> >> resulting in 28926 probesets, which is the number of probesets
you mention.
> >>
> >> 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
> >> _._._._._._._._._._._._._._._._._._
> >>
> >>
> >> Michael Walter wrote:
> >>
> >>> Dear List,
> >>>
> >>> I have another question with the xps package. I installed root
and xps, created the root schemes for the HuGene1.0 array and imported
the first CEL files following the example scripts. Everything works
fine to that point. However, after RMA normalization I'm missing a
couple of probesets. When I use the Affymetrix expression console you
get 33297 probesets. 4201 of these are +ve and -ve controls leaving
29096 probesets. With the xps package I have 28926 probesets with only
57 controls. Thus I'm missing 4371 and 227 probeset, respectively. I
already checked the archives and found a similar question. However,
the number of probesets i get is with exonlevel="all". I attached the
code and session info below. My question now is: Where are the missing
probesets, since I use the very same plg and clf files for xps and
expression console?
> >>>
> >>> Thanks for your thoughts,
> >>>
> >>> Michael
> >>>
> >>>
> >>> R code:
> >>>
> >>> library(xps)
> >>>
> >>> xpsdir = "C:/xps"
> >>> scmdir=paste(xpsdir, "schemes", sep="/")
> >>> libdir= paste(xpsdir, "library/HuGene10ST", sep="/")
> >>> anndir= paste(xpsdir, "annotation", sep="/")
> >>>
> >>>
> >>> scheme.hugene10stv1r4.na27 <- import.exon.scheme(
> >>> "Scheme_HuGene10stv1r4_na27_2",
> >>> filedir=scmdir,
> >>> layoutfile=paste(libdir,"HuGene-1_0-st-v1.r4.clf",sep="/"),
> >>> schemefile=paste(libdir,"HuGene-1_0-st-v1.r4.pgf",sep="/"),
> >>> probeset=paste(anndir,"HuGene-
1_0-st-v1.na27.2.hg18.probeset.csv",sep="/"),
> >>> transcript=paste(anndir,"HuGene-
1_0-st-v1.na27.hg18.transcript.csv",sep="/"),
> >>> verbose=TRUE)
> >>>
> >>> celdir <- getwd()
> >>>
> >>> scheme.HuGene10 <- root.scheme(paste("C:/xps/schemes","Scheme_Hu
Gene10stv1r4_na27_2.root",sep="/"))
> >>> data.test <- import.data(scheme.HuGene10, "DataTest",
celdir=celdir)
> >>> str(data.test)
> >>>
> >>> data.test2 <- attachMask(data.test)
> >>> data.test2 <- attachInten(data.test)
> >>>
> >>> data.test2 <- removeInten(data.test2)
> >>> data.test2 <- removeMask(data.test2)
> >>>
> >>> data.rma <- rma(data.test2, "tmpdt_Test2RMA",
background="antigenomic", normalize=T,
> >>> exonlevel="all", verbose = FALSE)
> >>>
> >>> expr.rma <- validData(data.rma)
> >>>
> >>> call.dabg <- dabg.call(data.test2,
"tmpdt_Test2DABG",exonlevel="all", verbose = FALSE)
> >>>
> >>> Session Info:
> >>>
> >>> R version 2.8.1 (2008-12-22)
> >>> i386-pc-mingw32
> >>>
> >>> locale:
> >>> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_M
ONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
> >>>
> >>> attached base packages:
> >>> [1] stats graphics grDevices utils datasets methods
base
> >>>
> >>> other attached packages:
> >>> [1] xps_1.2.6
> >>>
> >>>
> >>>
> >> _______________________________________________
> >> 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
> >>
> >>
> >
> >
>
> _______________________________________________
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>
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>
--?
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