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?
thanks in advance for any help
Andreia
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