I've become quite fond of affyQAReport and have numerous examples of cases
where I have used it to help identify problem arrays that my core facility,
which uses only Affymetrix tools, have said are fine. I am now using the
Affy Rat Gene 1.0 ST array and apparently cannot convert it into an
affyBatch (required as input to affyQAReport) using the packages I have been
steered to for analysis (oligo and pdInfoBuilder) . Is there another package
or approach one can use to do QA on these newer chips? I did try hacking
affyQAReport, but ran into my own limitations when I got to the function qc,
which sets a cdf environment variable.

Mark
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Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219  Home
Skype:  mkimpel

"The real problem is not whether machines think but whether men do." -- B.
F. Skinner
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