You can use aroma affymetrix which does the normalization for you and can
summarize transcript expression values for you.

Here is a tutorial for you:

http://www.aroma-project.org/node/37

It doesn't tie in directly with xmapcore, but once you have the transcript
expression values for each transcript id, you can then just look it up on
the xmapcore genome browser.

Fong

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