[BioC] exprs() in Bioc 2.10

[Michael Morley]

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