[BioC] RMA XPS Problem on MoGene 1.0 ST

[cstrato]

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/032353.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/Frameworks/R.framework/Resources/library/xps/schemes/Scheme_MoGe10stv1r4_na31.root>
>>
>> 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/Frameworks/R.framework/Resources/library/xps/schemes/Scheme_MoGe10stv1r4_na31.root>
>>
>> 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=TRUE,xps.scheme=scheme.moge10stv1r4.na31)
>>
>>
>> Creating new temporary file<rootData/tmp_MoGene_Glio_RMA.root>...
>>
>> Opening file
>> </Library/Frameworks/R.framework/Resources/library/xps/schemes/Scheme_MoGe10stv1r4_na31.root>
>>
>> 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/Frameworks/R.framework/Resources/library/xps/schemes/Scheme_MoGe10stv1r4_na31.root>
>>
>> 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]]
>>
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>
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