Hello, I would like to make simple test with SpikeIn: (like Dilution) library(affy) library(affydata) data(SpikeIn) myprobesets <- geneNames(SpikeIn)[1:12] eset <- rma(SpikeIn,subset=myprobesets) but I get error message: >myprobesets <- geneNames(SpikeIn)[1:12] Error in geneNames(SpikeIn) : No direct or inherited method for function "geneNames" for this call which difference between Dilution and SpikeIn gives? How can I use MAS5, RMA and dChip for SpikeIn? Thanks, Mohammad Esad-Djou

> >myprobesets <- geneNames(SpikeIn)[1:12] > Error in geneNames(SpikeIn) : No direct or inherited method for function "geneNames" for this call > > which difference between Dilution and SpikeIn gives? How can I use MAS5, RMA and dChip for SpikeIn? SpikeIn is not an AffyBatch (therefore you can't use the same procedures as you can on Dilution), instead it is a different kind of object containing only the probe intensities for a single probeset across 12 arrays > SpikeIn ProbeSet object: id=AFFX-BioB-5_at pm= 20 probes x 12 chips