Hi,
sorry for the long delay.
On Mon, Apr 1, 2013 at 7:21 AM, <andreia.fons...@gmail.com> wrote:
> Dear forum,
>
> I am analyzing data of HuGene2.0-st arrays. I am using aroma for
> pre-processing and used limma for differential expression. However after
> multiple testing I lost significance so I want to perform variance based
> filtering to try to increase the power of my differential expression
> analysis. So for that I did:
>
> ces <- getChipEffectSet(plm)
>
> ChipEffectSet:
> Name: Jurkat_0_vs_over_2
> Tags: RBC,QN,RMA
> Path:
> Documents/analysis_affy_arrays/plmData/Jurkat_0_vs_over_2,RBC,QN,RMA/HuGene-2_0-st
> Platform: Affymetrix
> Chip type: HuGene-2_0-st,r3_binary,monocell
> Number of arrays: 6
> Names: Ju_0_1_1, Ju_0_2_2, Ju_0_3_3, ..., Ju_34c_5_6 [6]
> Time period: 2013-03-27 16:56:07 -- 2013-03-27 16:56:08
> Total file size: 3.08MB
> RAM: 0.01MB
> Parameters: {}
>
>
> eset <- extractExpressionSet(ces, verbose=-5);
>
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 53617 features, 6 samples
> element names: exprs
> protocolData: none
> phenoData: none
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation:
>
> but when I try to make
>
> nsFilter(eset) I get the following error:
>
> Error in if (nchar(annChip) == 0) stop("'eset' must have a valid annotation
> slot") :
> argument is of length zero
>
>
> what I am doing wrong?
The extractExpressionSet() method does not populate the 'annotation'
slot of the ExpressionSet automatically. The main reason for this is
that it should take different values depending if you wish to continue
doing analysis with the 'affy' package, the 'oligo' package and so on.
However, you can set it manually though, i.e.
eset@annotation <- "hugene20st";
As far as I understand it (I might be wrong), this will cause
genefilter::nsFilter() to look for the/a Bioconductor ChipDb
annotation package named 'hugene20st.db'. I'm not sure if
Bioconductor (or some else is providing such a package). For that,
please check with them over at the Bioconductor forums.
Hope this helps a bit,
Henrik
>
> thanks in advance for any help
>
> Andreia
>
>
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