[BioC] rma command error in oligo package

[James W. MacDonald]

Hi Maria,

On 4/22/2013 12:36 PM, Maria [guest] wrote:
> Hi everybody!
>
> I have been using the oligo package without any problem since a couple of months ago but now when I write the following commands the following error appears when I use the command rma
>
>> celFiles<-list.celfiles()
>> affyRaw<-read.celfiles(celFiles)
>> ppData<-rma(affyRaw)
> Error in function (classes, fdef, mtable)  :
>    unable to find an inherited method for function ‘probeNames’ for signature ‘"ExonFeatureSet"’
>
> I have no idea what is happen because last week everything worked properly, any suggestion?

It's because you have done something like

library(oligo)
library(affy)

which has caused the rma function in affy to come before the rma 
function from oligo in the search path.

You can either stop loading the affy package, or specify the rma 
function you want, using the :: accessor:

oligo::rma(affyRaw)

Best,

Jim


>
> Thank you!
>
> Maria
>
>
>   -- output of sessionInfo():
>
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.2          DBI_0.2-5
>   [4] estrogen_1.8.9          affy_1.36.1             oligo_1.22.0
>   [7] oligoClasses_1.20.0     PREDA_1.4.0             annotate_1.36.0
> [10] AnnotationDbi_1.20.7    multtest_2.14.0         lokern_1.1-3
> [13] Biobase_2.18.0          BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>   [1] affxparser_1.30.2     affyio_1.26.0         BiocInstaller_1.8.3
>   [4] Biostrings_2.26.3     bit_1.1-10            codetools_0.2-8
>   [7] ff_2.2-11             foreach_1.4.0         GenomicRanges_1.10.7
> [10] IRanges_1.16.6        iterators_1.0.6       MASS_7.3-23
> [13] parallel_2.15.3       preprocessCore_1.20.0 sfsmisc_1.0-23
> [16] splines_2.15.3        stats4_2.15.3         survival_2.37-4
> [19] tools_2.15.3          XML_3.96-1.1          xtable_1.7-1
> [22] zlibbioc_1.4.0
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099