[BioC] Yeast 2.0 Arrays - alternative ways

[Mike Walter]

Hi Jim,

>I wonder if some of the things in the mask file don't actually exist on 
>the chip? If I try this using the Dilution data, there are no problems:
>
> > rma(Dilution, subset = featureNames(Dilution)[1:250])
>Background correcting
>Normalizing
>Calculating Expression
>ExpressionSet (storageMode: lockedEnvironment)
>assayData: 250 features, 4 samples
>   element names: exprs
>protocolData: none
>phenoData
>   sampleNames: 20A, 20B, 10A, 10B
>   varLabels and varMetadata description:
>     liver: amount of liver RNA hybridized to array in micrograms
>     sn19: amount of central nervous system RNA hybridized to array in 
>micrograms
>
>     scanner: ID number of scanner used
>featureData: none
>experimentData: use 'experimentData(object)'
>Annotation: hgu95av2
>
>However, if I add some random fake probeset ID, I get a segfault as well:
>
> > rma(Dilution, subset = c(featureNames(Dilution)[1:250], "10432_s_at"))
>Background correcting
>
>Process C:/R-patched/bin/rterm.exe exited abnormally with code 5 at Fri 
>Jul 09 10:40:12 2010
>
>So I would first check that all the row names of your msk.sp data.frame 
>are actually featureNames of your AffyBatch:
>
>all(rownames(msk.sp) %in% featureNames(d2))
>
>and if not, subset the offending rownames first.
>
>Best,
>
>Jim
You are perfectly right. There is one probeset in the S. pombe mask file that does not exist in the affybatch feature names. By excluding this I can run RMA on the S. cerevisiae probes only. Thanks a lot and best wishes,

Mike