[BioC] Summarization methods for affy genechip expression data

[Joern Toedling]

Hello,

one way to do this, is to create a custom object of class "cdfenv" that
is used during preprocessing and contains the probe to probe-set
mapping. Package affy contains a vignette "dealing_with_cdfenvs" that
provides some insight into this process and example data
"cdfenv.example", which shows you how such an environment is going to
look like. The vignette also tells you how to associate your AffyBatch
raw data to the new, custom cdfenv instead of the standard Affymetrix
one, which is build from their chip description file (.CDF).

Regards,
Joern

zhi.zhang at syngenta.com wrote:
> Dear All,
>
> I am trying to use a summarization method alone to condense my affy
> genechip expression data. The RNA in this experiment was pretty bad, so
> I filtered a few poor performing probes in each probeset. Now I got the
> PM intensity matrix with various probes in each probeset, and tried to
> summarize the probeset.  I checked the summarization methods in affy
> package, but couldn't find a proper one. I am still confused if there
> was a summarization method that can be used to condense this filtered
> dataset. Anyone has this experience?
>
> Best,
>
>
> Zhi Zhang
> Lead Selection
> Applied Genomics
>
> Syngenta Biotechnology, Inc.
> 3054 Cornwallis Road
> Research Triangle Park, NC 27709-2257
>
> Tel: (919)765-5052
> Fax: (919)541-8585
>