Dear Zack, The probeset annotation file for the exon arrays contains a column "level", which was set to "" for whole genome arrays. In version na31 Affymetrix has now set "level" to "---". This change caused the problem which is now solved in the new version xps_1.10.1 which is available from BioC 2.7. Best regards Christian On 10/12/10 10:30 PM, cstrato wrote: > Dear Zack, > > Meanwhile I could repeat your results when using the new annotation > files version na31. However, when I use the old annotation files na30 > then everything is ok. This means that there may be a problem with the > new annotation files. I need to investigate further and will let you > know. Meanwhile I suggest that you use the annotation files na30. > > Best regards > Christian > > > On 10/11/10 9:55 PM, cstrato wrote: >> Dear Zack, >> >> Usually you get this result when you create the scheme file for MoGene >> using "import.genome.scheme" instead of using "import.exon.scheme", see >> e.g.: >> https://www.stat.math.ethz.ch/pipermail/bioconductor/2010-March/032 353.html >> >> >> However, it seems that you have created the scheme correctly. Thus could >> you please send me the output of: >> > str(scheme.moge10stv1r4.na31) >> >> Which version of the Affymetrix annotation files did you use to create >> "scheme.moge10stv1r4.na31"? >> You need to use the annotation files created on 09/08/10 and not the >> ones created on 08/30/10 since the older files have additional >> "control->affx" which are "neg_control". >> >> Another problem could be your code: >> > data.rma <-rma(data.moge, ...., xps.scheme=scheme.moge10stv1r4.na31) >> >> Since "xps.scheme" should only be used if you want to use alternative >> CDF-files for expression arrays, you should do: >> > data.rma <-rma(data.moge, ...., xps.scheme=NULL) >> >> Please send me: >> - your sessionInfo(), >> - the output of str(scheme.moge10stv1r4.na31), >> - the output of str(data.rma), >> and let me know >> - which annotation files you have used and >> - whether rma(.., xps.scheme=NULL) solves the problem. >> >> 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 >> _._._._._._._._._._._._._._._._._._ >> >> >> On 10/11/10 5:07 PM, Zack Liu wrote: >>> Dear members, >>> >>> I have encountered some problems using XPS library on Mouse Gene 1.0 ST >>> arrays.. Basically, when I run rma on my cel files, the signal matrix >>> only >>> have 21 rows (probeset?) for all the samples. Has anybody here had the >>> same >>> problem before? >>> >>> ## Generate the Scheme file >>> >>> scmdir<- paste(.path.package("xps"),"schemes",sep="/") >>> >>> libdir<- "./Affy/libraryfiles" >>> >>> anndir<- "./Affy/Annotation" >>> >>> >>> scheme.moge10stv1r4.na31<- >>> import.exon.scheme("Scheme_MoGe10stv1r4_na31", >>> filedir=scmdir, layoutfile=paste(libdir, >>> "MoGene-1_0-st-v1.r4.clf",sep="/"),schemefile=paste(libdir, >>> "MoGene-1_0-st-v1.r4.pgf",sep="/"), probeset=paste(anndir, >>> "MoGene-1_0-st-v1.na31.mm9.probeset.csv",sep="/"), >>> transcript=paste(anndir,"MoGene- 1_0-st-v1.na31.mm9.transcript.csv",sep="/")) >>> >>> >>> >>> >>> ### Generate the signal file >>> >>> >>> celDir<- "./rawData/tissues/MoGene-1-0-st-v1/" >>> >>> celfiles<- c("001.CEL","002.CEL","003.CEL") >>> >>> celNames<- c("01","02","03") >>> >>> datdir<-"rootData" >>> >>> >>> data.moge<- import.data(scheme.moge10stv1r4.na31,"mogene_glio",filedir= >>> datdir,celdir=celDir,celfiles=celfiles,celnames =celNames,verbose=T) >>> >>> >>> data.moge<- attachInten(data.moge) >>> >>> tmp<- intensity(data.moge) >>> >>> head(tmp) >>> >>>> dim(tmp) >>> >>> [1] 1102500 5 >>> >>> >>> ### So far so good, I have >>> >>> #### Problem starts here >>> >>> data.rma<-rma(data.moge, "tmp_MoGene_Glio_RMA",filedir=datdir,tmpdir="", >>> option ="transcript", background="antigenomic",normalize=TRUE,exonlevel= >>> "all",verbose=TRUE,xps.scheme=scheme.moge10stv1r4.na31) >>> >>> >>> Creating new temporary file<rootdata tmp_mogene_glio_rma.root="">... >>> >>> Opening file >>> </library> >>> >>> >>> in<read> mode... >>> >>> Opening file<./rootData/mogene_glio_cel.root> in<read> mode... >>> >>> Added<3> trees to PreprocesSet. >>> >>> Preprocessing data using method<preprocess>... >>> >>> Background correcting raw data... >>> >>> setting selector mask for typepm<16316> >>> >>> calculating background for<01.cel>... >>> >>> background statistics: >>> >>> 1087986 cells with minimal intensity 0 >>> >>> 970 cells with maximal intensity 84.8093 >>> >>> calculating background for<02.cel>... >>> >>> background statistics: >>> >>> 1087986 cells with minimal intensity 0 >>> >>> 4596 cells with maximal intensity 82.8614 >>> >>> calculating background for<03.cel>... >>> >>> background statistics: >>> >>> 1087986 cells with minimal intensity 0 >>> >>> 3018 cells with maximal intensity 71.3567 >>> >>> Normalizing raw data... >>> >>> normalizing data using method<quantile>... >>> >>> setting selector mask for typepm<16316> >>> >>> finished filling<3> arrays. >>> >>> computing common mean... >>> >>> finished filling<3> trees. >>> >>> Converting raw data to expression levels... >>> >>> summarizing with<medianpolish>... >>> >>> setting selector mask for typepm<16316> >>> >>> setting selector mask for typepm<16316> >>> >>> calculating expression for<21> of<35556> units...Finished. >>> >>> expression statistics: >>> >>> minimal expression level is<36.657> >>> >>> maximal expression level is<14222.3> >>> >>> preprocessing finished. >>> >>> Opening file >>> </library> >>> >>> >>> in<read> mode... >>> >>> Opening file<rootdata tmp_mogene_glio_rma.root=""> in<read> mode... >>> >>> Opening file<rootdata tmp_mogene_glio_rma.root=""> in<read> mode... >>> >>> Exporting data from tree<*> to file<rootdata tmp_mogene_glio_rma.txt="">... >>> >>> Reading entries from<mogene-1_0-st-v1.ann> ...Finished >>> >>> <21> of<21> records exported. >>> >>>> >>> >>>> >>> >>>> >>> >>>> dim(tmp) >>> >>> Error: object 'tmp' not found >>> >>>> >>> >>>> data.moge<- attachInten(data.moge) >>> >>> tmp<- intensity(data.moge) >>> >>> head(tmp) >>> >>> >>> >>> >>>> tmp<- intensity(data.moge) >>> >>>> head(tmp) >>> >>> X Y 01.cel_MEAN 02.cel_MEAN 03.cel_MEAN >>> >>> 1 0 0 6213 8575 6339 >>> >>> 2 1 0 105 198 126 >>> >>> 3 2 0 6361 8720 6278 >>> >>> 4 3 0 138 170 120 >>> >>> 5 4 0 138 180 134 >>> >>> 6 5 0 127 139 133 >>> >>>> >>> >>>> >>> >>>> >>> >>>> dim(tmp) >>> >>> [1] 1102500 5 >>> >>>> >>> >>>> >>> >>>> data.rma<-rma(data.moge, >>> "tmp_MoGene_Glio_RMA",filedir=datdir,tmpdir="",option ="transcript", >>> background="antigenomic",normalize=TRUE,exonlevel="all",verbose=TR UE,xps.scheme=scheme.moge10stv1r4.na31) >>> >>> >>> >>> Creating new temporary file<rootdata tmp_mogene_glio_rma.root="">... >>> >>> Opening file >>> </library> >>> >>> >>> in<read> mode... >>> >>> Opening file<rootdata mogene_glio_cel.root=""> in<read> mode... >>> >>> Added<3> trees to PreprocesSet. >>> >>> Preprocessing data using method<preprocess>... >>> >>> Background correcting raw data... >>> >>> setting selector mask for typepm<16316> >>> >>> calculating background for<01.cel>... >>> >>> background statistics: >>> >>> 1087986 cells with minimal intensity 0 >>> >>> 970 cells with maximal intensity 84.8093 >>> >>> calculating background for<02.cel>... >>> >>> background statistics: >>> >>> 1087986 cells with minimal intensity 0 >>> >>> 4596 cells with maximal intensity 82.8614 >>> >>> calculating background for<03.cel>... >>> >>> background statistics: >>> >>> 1087986 cells with minimal intensity 0 >>> >>> 3018 cells with maximal intensity 71.3567 >>> >>> Normalizing raw data... >>> >>> normalizing data using method<quantile>... >>> >>> setting selector mask for typepm<16316> >>> >>> finished filling<3> arrays. >>> >>> computing common mean... >>> >>> finished filling<3> trees. >>> >>> Converting raw data to expression levels... >>> >>> summarizing with<medianpolish>... >>> >>> setting selector mask for typepm<16316> >>> >>> setting selector mask for typepm<16316> >>> >>> calculating expression for<21> of<35556> units...Finished. >>> >>> expression statistics: >>> >>> minimal expression level is<36.657> >>> >>> maximal expression level is<14222.3> >>> >>> preprocessing finished. >>> >>> Opening file >>> </library> >>> >>> >>> in<read> mode... >>> >>> Opening file<rootdata tmp_mogene_glio_rma.root=""> in<read> mode... >>> >>> Opening file<rootdata tmp_mogene_glio_rma.root=""> in<read> mode... >>> >>> Exporting data from tree<*> to file<rootdata tmp_mogene_glio_rma.txt="">... >>> >>> Reading entries from<mogene-1_0-st-v1.ann> ...Finished >>> >>> <21> of<21> records exported. >>> >>> >>>> expr.rma<- validData(data.rma) >>> >>>> dim(expr.rma) >>> >>> [1] 21 3 >>> >>> >>> ## only 21 records.... >>> >>> >>> Can anyone help? Thank you! >>> >>> >>> Zach Liu >>> >>> >>> Genomics& Computational Biology Program >>> Abramson Cancer Institute, School of Medicine >>> University of Pennsylvania >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 >