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

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