[BioC] oligo package

[James W. MacDonald]

Hi Bruno,

On 12/6/2012 12:05 PM, Bruno [guest] wrote:
> Hi all,
> I've been working on R/Bioconductor for the last month and i'm still quite confused on many ways. Im currently trying to process an expression microarray dataset with Affymetrix chip (hugene.1.1.st.v1). Questions are actually multiple. I get an error when im trying to load the phenodata with the read.celfiles command saying sample names are different between phenodata and protocol data and phenodata and featuredata:
> Error in validObject(out) :
>    invalid class “GeneFeatureSet” object: 1: sampleNames differ between assayData and phenoData
> invalid class “GeneFeatureSet” object: 2: sampleNames differ between phenoData and protocolData
>   Also i have no clues how to annotate my expression data as i cant even find commands to access the annotation package. Sorry for the non-precise questions. I tried to read as much as i could and asked everyone in the dep but im still stuck here. Thank you very much

There isn't really a problem with your questions, but you don't give us 
enough to go on. When asking questions, you have to always think about 
what information will be useful to those who might answer.

I can pretty much condense what you have told us into 'I did some stuff 
and here are the errors'. But what you aren't telling us is EXACTLY what 
did you do? And the only way to really tell us is to copy and paste the 
R commands you are using, right up to the point you get the error.

So show us your code, and perhaps we can help.

Best,

Jim


> Bruno
>
>   -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-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.hugene.1.1.st.v1_3.8.0 RSQLite_0.11.2
> [3] DBI_0.2-5                 oligo_1.22.0
> [5] Biobase_2.18.0            oligoClasses_1.20.0
> [7] BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
>   [1] affxparser_1.30.0     affyio_1.26.0         BiocInstaller_1.8.3
>   [4] Biostrings_2.26.2     bit_1.1-9             codetools_0.2-8
>   [7] ff_2.2-10             foreach_1.4.0         GenomicRanges_1.10.5
> [10] IRanges_1.16.4        iterators_1.0.6       parallel_2.15.1
> [13] preprocessCore_1.20.0 splines_2.15.1        stats4_2.15.1
> [16] tools_2.15.1          zlibbioc_1.4.0
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099