Dear all,

I fairly new to the field of Exon Arrays and my experiences with
Microarrays in general are quite limited, so I have a couple of
questions concerning the analysis of Exon Array data.

First of all, I would like to do an RMA (or GCRMA) based on the
validated genes of the core probeset (so bg, qn + sum). The way I
understood the literature, this normalizes ALL probesets based on the
intensity values of the core probeset (which is also what I intend to
do). Afterwards, I want to extend my analysis on the full probeset, as
I will focus on some genes that are not included in 'core'.
I read about this procedure in a paper on APT and R by H. Lockstone
and wanted to implement it via aroma.

Am I mislead in this case?
I tried to realize this by doing a GCRMA on 'core', but the resulting
probe intensities are to few (~285k) and the probes I'm looking for
are not included.

Before that, I did a regular RMA on the full probeset and I got all
the probes /the intensities I was looking for, but I realized that
normalizing to not validated genes may not be the best idea.

It would be a great help if you could set my thoughts straight and if
I'm correct tell me how to use aroma to achieve what I want.

Note: I assembled my script as described in

Thank you in advance for your help.

With best regards,

When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.

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