I am analyzing an Affymetrix array dataset. After RMA normalization the data is returned as an
expressionSet object. However, I am not able to replace the expression value 'slot' with some new data anymore, although this did work before (BioC 3.3). See example below. Any suggestions on how to do this in BioC 3.4? Thanks.
--> The normalized data I get is REFSEQ-based, but I am averaging (collapsing) the data on the level of ENTREZG IDs, which I then would like to 'put back' in the
expressionSet. The number of genes/features is reduced from ~60k to ~20k. All other (meta)data is not affected.
> library(Biobase) > sample.data <- ExpressionSet(assayData=matrix(runif(1000), nrow=100, ncol=10)) > sample.data ExpressionSet (storageMode: lockedEnvironment) assayData: 100 features, 10 samples element names: exprs protocolData: none phenoData: none featureData: none experimentData: use 'experimentData(object)' Annotation: > replacement <- matrix(runif(750), nrow=75, ncol=10) > exprs(sample.data) <- replacement Error in .validate_assayDataElementReplace(obj, value) : object and replacement value have different dimensions >
> sessionInfo() R version 3.3.1 Patched (2016-10-18 r71535) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  Biobase_2.34.0 BiocGenerics_0.20.0 >