Hello everyone, I'm reading affy data using ReadAffy and have just noticed that the total number of probes listed in the intensity table is about 10k larger than the number of probes associated with probesets - at least as returned by indexProbes (see example below). I'm wondering if this is how it is supposed to be - and if so, whether these "orphan" probes are used in any way by any standard analysis procedures? esExpDesc <- read.AnnotatedDataFrame("experimentDescription.txt", esPath, header=TRUE, sep = "\t", stringsAsFactors = TRUE, row.names=1) esAffyExp <- ReadAffy(filenames = rownames(pData(esExpDesc)), phenoData = esExpDesc, celfile.path = esPath, verbose = TRUE) nrow(exprs(esAffyExp)) #[1] 1004004 length(unlist(indexProbes(esAffyExp, which="both"))) #[1] 992936 Many thanks Mikhail == Mikhail Spivakov PhD European Bioinformatics Institute Hinxton UK [[alternative HTML version deleted]]