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@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@mail.med.upenn.edu
>> Phone: 215-898-2026
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@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@mail.med.upenn.edu
Phone: 215-898-2026


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