Entering edit mode
Mikhail Spivakov
▴
30
@mikhail-spivakov-3913
Last seen 10.1 years ago
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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