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Vicky Fan
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10
@vicky-fan-5789
Last seen 10.5 years ago
Dear all,
I am using the 'oligo' package to process data from Affymetrix miRNA
v3.0 arrays. When I extract the probe names as follows, I get 243982
probes:
> library(oligo)
> celFiles <- list.celfiles()
> rawData <- read.celfiles(celFiles)
> pNames <- probeNames(rawData)
> exprs.rawData <- exprs(rawData)
However, extracting the data itself gives me a different number of
rows:
> length(pNames)
[1] 243982
> dim(exprs.rawData)
[1] 292681 6
Ive verified that this result occurs using the sample CEL files from
the Affymetrix website here (although there is a login required):
http://www.affymetrix.com/Auth/support/downloads/demo_data/mirna_3_sam
ple_data.zip
Shouldnt the number of probes in the CEL file be the same as the
number of rows in the dataset? Im aware that the exprs function is
for objects of type eSet and that read.celfiles returns an
ExpressionFeatureSet object, not an eSet object, so maybe this has
something to do with the non-matching numbers.
Regards,
Vicky
--
Vicky Fan
Research Programmer
Bioinformatics Institute
School of Biological Sciences
University of Auckland
Ph: 09 373 7599 x 83777
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