Perfect! Thank you. On 04/18/2012 09:03 AM, Benilton Carvalho wrote: > Hi Mike, > > I'll work on a permanent solution for this. In the meantime, please > load the Biobase package explicitly, as in: > > library(Biobase) > library(oligo) > > and everything should work as expected. > > b > > On 18 April 2012 13:56, Michael Morley<mmorley at="" mail.med.upenn.edu=""> wrote: >> Hi Benilton, >> >> One other thing is this command works.. >> >> exprs(eset)[1:2,] >> >> >> >> >> Here's my sessionInfo() >> >> R version 2.15.0 (2012-03-30) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> LC_MONETARY=en_US.UTF-8 >> [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C >> LC_NAME=C LC_ADDRESS=C >> LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] pd.mogene.1.0.st.v1_3.6.0 RSQLite_0.11.1 >> DBI_0.2-5 limma_3.12.0 oligo_1.20.1 >> [6] oligoClasses_1.18.0 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.28.0 affyio_1.24.0 Biobase_2.16.0 >> BiocGenerics_0.2.0 BiocInstaller_1.4.3 Biostrings_2.24.1 >> [7] bit_1.1-8 codetools_0.2-8 ff_2.2-6 >> foreach_1.4.0 IRanges_1.14.2 iterators_1.0.6 >> [13] preprocessCore_1.18.0 splines_2.15.0 stats4_2.15.0 >> tools_2.15.0 zlibbioc_1.2.0 >> >> >> >> On 04/18/2012 08:04 AM, Benilton Carvalho wrote: >> >> Hi Mike, >> >> can you please give the results for sessionInfo() ? >> >> it looks like that 'exprs<-' isnt visible for you... >> >> benilton >> >> On 17 April 2012 21:25, Michael Morley<mmorley at="" mail.med.upenn.edu=""> wrote: >> >> USing oligo package for RMA probe summaries on Affy Mouse Gene 1.1 array. >> This code work previously, I basically use it to filter out low expressed >> genes and control probes. >> >> >> affyGeneFS<- read.celfiles(celFiles,verbose=TRUE) >> >> ## Get a list of control probes >> con<- db(pd.mogene.1.0.st.v1) >> mainprobes<- dbGetQuery(con, "select DISTINCT transcript_cluster_id from >> featureSet where type=1 and transcript_cluster_id>1;") >> mainprobes<- as.character(mainprobes$transcript_cluster_id) >> >> >> eset = rma(affyGeneFS,target='core') >> apcall = apply(exprs(eset)[mainprobes,],1,function(x) if (sum(x> 3.8) ==0 ) >> FALSE else TRUE ) >> >> >> exprs(eset)=exprs(eset)[rownames(as.data.frame(apcall[apcall==TRUE] )),] >> >> The last line gives me: >> >> Error in exprs(eset) = exprs(eset)[rownames(as.data.frame(apcall[apcall == >> : >> could not find function "exprs<-" >> >> Can I no longer set the expressionset slot this way? Should I be using a >> different way to begin with? >> >> Thanks >> >> Mike >> >> >> -- >> Michael P Morley >> Senior Bioinformatics Specialist >> Penn Cardiovascular Institute >> Translational Research Center,Cubicle 11-114A >> 3400 Civic Center Blvd, Bldg 421 >> Philadelphia,PA 19104-5159 >> Email: mmorley at mail.med.upenn.edu >> Phone: 215-898-2026 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> Michael P Morley >> Senior Bioinformatics Specialist >> Penn Cardiovascular Institute >> Translational Research Center,Cubicle 11-114A >> 3400 Civic Center Blvd, Bldg 421 >> Philadelphia,PA 19104-5159 >> Email: mmorley at mail.med.upenn.edu >> Phone: 215-898-2026 -- Michael P Morley Senior Bioinformatics Specialist Penn Cardiovascular Institute Translational Research Center,Cubicle 11-114A 3400 Civic Center Blvd, Bldg 421 Philadelphia,PA 19104-5159 Email: mmorley at mail.med.upenn.edu Phone: 215-898-2026