Hi all,

I am using aroma.affymetrix for an analysis on Human Exon Array data
and would need to access the individual probe intensities mapped to
probe_id after background correction and normalization. Is there an
easy way to do this? Below you can see what I have tried so far.

With the notation on http://www.aroma-project.org/node/37 I am looking
at object csN - data at probe-level after BC and QN

> affyBatch <- extractAffyBatch(csN)
         # I get an error message about package "huex10stv2cdf" not being
available from Bioconductor.
> probes_matrix <- extractMatrix(csN, cells=NULL, field=c("intensities", 
> "stdvs", "pixels"), drop=FALSE, verbose=verbose)       # I do not get any 
> information about which probe the intensity belongs to
> intensities <- getIntensities(csN)
        # no probe or array information
> unitIntensities <- getUnitIntensities(csN, verbose=verbose)
        # I get transcript and probeset information and the individual
intensities of the 4 probes in each probeset, but numbered 1 to 4, so
I still cannot map them to their target sequence.

I have now run out of ideas so I would really appreciate any
suggestions. Thank you very much in advance for your help.

Best regards,
Maria Rodrigo

PhD student in Biostatistics
Department of Haematology, Medical Center Aalborg Hospital Science and
Innovation Center AHSIC Denmark

When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
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