[BioC] exprs() in Bioc 2.10

[Benilton Carvalho]

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
>
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