[BioC] RMA XPS Problem on MoGene 1.0 ST
cstrato
cstrato at aon.at
Mon Oct 11 21:55:20 CEST 2010
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]]
>
> _______________________________________________
> 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
>
More information about the Bioconductor
mailing list