[BioC] RMA, d-chip and Plier for new chip type Human/Mouse/Rat Gene

Henrik Bengtsson hb at stat.berkeley.edu
Tue Feb 26 02:47:46 CET 2008

The aroma.affymetrix package can do RMA and imitate MBEI ("dChip") as
long as you've got CEL files and a CDF file.  For more information and
questions, go to:


Note that there is active research/development on alternative-splicing
("FIRMA") added to the package (work by Elizabeth Purdom, Mark
Robinson and formerly by Ken Simpson; Berkeley/WEHI), especially for
the Human Exon 1.0 ST chip type.  Make sure you know about the
customized CDFs (still same chip type) they use for this analysis
before you start.



On Mon, Feb 25, 2008 at 4:59 PM, Fang, Hong* <hong.fang at fda.hhs.gov> wrote:
> Dear Murim:
>  I am still waiting for Bioconductor's answer!
>  Thank you for contacting with us! So, we know that we are not alone!
>  Best Regard's
>  Hong
>  -----Original Message-----
>  From: Murim Choi [mailto:murim.choi at yale.edu]
>  Sent: Monday, February 25, 2008 12:33 PM
>  To: Fang, Hong*
>  Subject: Bioconductor
>  Dear Dr. Fang,
>  I just found your post on Bioconductor maillist.
>  Subject: RMA, d-chip and Plier for new chip type Human/Mouse/Rat Gene
>  1.0 ST Array
>  Actually I was having a sample problem with you, so I was wondering
>  you found any answer for this question..
>  Thank you in advance,
>  Murim
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