[BioC] exprs() in Bioc 2.10

[Benilton Carvalho]

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