Question: RMA error in cdf environment with removed probes (Yeast2)
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gravatar for Omri Yahel
10.5 years ago by
Omri Yahel70
Omri Yahel70 wrote:
Hello I am encountering an error during RMA of an affybatch. I have used RemoveProbes.r to remove all S. pombe probesets and 864 individual S.cerevisiae probes from the yeast2 platform. >data<-ReadAffy() > data AffyBatch object size of arrays=496x496 features (11 kb) cdf=Yeast_2 (5900 affyids) number of samples=26 number of genes=5900 annotation=yeast2 notes= > > length(pm(data[,1])) [1] 64688 When I attempt to compute the eset > eset <- rma(data) Background correcting Normalizing Calculating Expression Error in rma(data) : length of 'dimnames' [1] not equal to array extent I assume this has something to do with the removal of individual probes from the environment, but am not sure and do not know how to remedy this. Any help appreciated Omri Yahel MSc student School of Biological Sciences University of Auckland, New Zealand [[alternative HTML version deleted]]
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ADD COMMENTlink modified 10.5 years ago by Jenny Drnevich1.9k • written 10.5 years ago by Omri Yahel70
Answer: RMA error in cdf environment with removed probes (Yeast2)
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gravatar for Jenny Drnevich
10.5 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:
Hi Omri, I'm assuming that the RemoveProbes.r function is the one I have posted to the Bioconductor mailing list several times, mostly recently with some changes on Sept 24, 2008? https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html If so, would you post your entire session, including the code you used to remove the probe sets and probes, along with your sessionInfo()? That should give us more details so we can help you. Thanks, Jenny At 10:08 PM 12/16/2008, Omri Yahel wrote: >Hello > >I am encountering an error during RMA of an affybatch. >I have used RemoveProbes.r to remove all S. pombe probesets and 864 >individual S.cerevisiae probes from the yeast2 platform. > > >data<-ReadAffy() > > data >AffyBatch object >size of arrays=496x496 features (11 kb) >cdf=Yeast_2 (5900 affyids) >number of samples=26 >number of genes=5900 >annotation=yeast2 >notes= > > > > length(pm(data[,1])) >[1] 64688 > > >When I attempt to compute the eset > > > eset <- rma(data) >Background correcting >Normalizing >Calculating Expression >Error in rma(data) : length of 'dimnames' [1] not equal to array extent > >I assume this has something to do with the removal of individual probes from >the environment, but am not sure and do not know how to remedy this. >Any help appreciated > >Omri Yahel >MSc student >School of Biological Sciences >University of Auckland, New Zealand > > [[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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu
ADD COMMENTlink written 10.5 years ago by Jenny Drnevich1.9k
here is the code for the issue I am having. Thanks again for you help > > length(pm(data[,1])) [1] 120855 > > > #############remove selected S. cerevisiae probe Ids > > > > source("RemoveProbesNew.r") > library(yeast2cdf) > library(yeast2probe) > cleancdf <- cleancdfname("yeast2",addcdf=FALSE) > ResetEnvir(cleancdf) Loading required package: yeast2cdf Loading required package: yeast2probe > > RemoveProbes(listOutProbes[1:233],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[233:467],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[467:500],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[500:600],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[600:640],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[640:650],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[650:700],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[700:710],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[710:720],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[720:800],listOutProbeSets=NULL, cleancdf) > RemoveProbes(listOutProbes[800:884],listOutProbeSets=NULL, cleancdf) > length(pm(data[,1])) [1] 119991 > >######listOutProbes is a character vector of probe ID's. I don't know why I had to subset it like this, putting the >######whole vector in, or larger subsets gave; >######> RemoveProbes(listOutProbes,listOutProbeSets=NULL, cleancdf) ####### Error in ans[[i]][, i.probes] : incorrect number of dimensions > > > > > >############remove s. pombe probesets > > > > s_cerevisiae<-scan("s_cerevisiae.msk", skip=2, list("", "")) Read 5028 records > pombe_filter_out<-s_cerevisiae[[1]] #the probesets you DONT want. > > > source("RemoveProbesNew.r") > library(yeast2cdf) > library(yeast2probe) > cleancdf <- cleancdfname("yeast2",addcdf=FALSE) > RemoveProbes(listOutProbes=NULL, pombe_filter_out, cleancdf) > length(pm(data[,1])) [1] 64688 ? > >#################################read in the new data and do the RMA > > > pd<-read.AnnotatedDataFrame("targets.txt",header=TRUE,row.names=1,as .is=TRUE) # reads the names from the targets file > data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd) # reads all .CEL files in the working directory and assigns them names from the target files > > eset <- rma(data)#does the normalisation Background correcting Normalizing Calculating Expression Error in rma(data) : length of 'dimnames' [1] not equal to array extent > > > > > traceback() 2: .Call("rma_c_complete", pm(object, subset), pNList, ngenes, normalize, background, bgversion, verbose, PACKAGE = "affy") 1: rma(data) > > > > > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.1252;LC_MONETARY=English_New Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] yeast2probe_2.3.0 yeast2cdf_2.3.0 matchprobes_1.14.0 [4] yeast2.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 [7] AnnotationDbi_1.4.2 affy_1.20.0 Biobase_2.2.1 [10] limma_2.16.3 loaded via a namespace (and not attached): [1] affyio_1.10.1 preprocessCore_1.4.0 > Omri Yahel On Thu, Dec 18, 2008 at 4:04 AM, Jenny Drnevich <drnevich@illinois.edu>wrote: > Hi Omri, > > I'm assuming that the RemoveProbes.r function is the one I have posted to > the Bioconductor mailing list several times, mostly recently with some > changes on Sept 24, 2008? > https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296.html > > If so, would you post your entire session, including the code you used to > remove the probe sets and probes, along with your sessionInfo()? That should > give us more details so we can help you. > > Thanks, > Jenny > > > At 10:08 PM 12/16/2008, Omri Yahel wrote: > >> Hello >> >> I am encountering an error during RMA of an affybatch. >> I have used RemoveProbes.r to remove all S. pombe probesets and 864 >> individual S.cerevisiae probes from the yeast2 platform. >> >> >data<-ReadAffy() >> > data >> AffyBatch object >> size of arrays=496x496 features (11 kb) >> cdf=Yeast_2 (5900 affyids) >> number of samples=26 >> number of genes=5900 >> annotation=yeast2 >> notes= >> > >> > length(pm(data[,1])) >> [1] 64688 >> >> >> When I attempt to compute the eset >> >> > eset <- rma(data) >> Background correcting >> Normalizing >> Calculating Expression >> Error in rma(data) : length of 'dimnames' [1] not equal to array extent >> >> I assume this has something to do with the removal of individual probes >> from >> the environment, but am not sure and do not know how to remedy this. >> Any help appreciated >> >> Omri Yahel >> MSc student >> School of Biological Sciences >> University of Auckland, New Zealand >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich@illinois.edu > [[alternative HTML version deleted]]
ADD REPLYlink written 10.5 years ago by Omri Yahel70
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