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

I’ve 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_sample_data.zip

Shouldn’t the number of probes in the CEL file be the same as the number of rows in the dataset?  I’m 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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