[BioC] exprs() in Bioc 2.10

[Michael Morley]

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
>>
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>>
>>
>> --
>> 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