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

Fang, Hong* hong.fang at fda.hhs.gov
Tue Feb 26 16:03:52 CET 2008

 Hi, Henrik:

Thanks for the information!

How about Plier? Which is very popular used method recently?

Best Regards,


Dr. Hong Fang 
Senior Technical Specialist
Manger, Bioinformatics 
ICF International at NCTR 
National Center for Toxicological Research (NCTR) 
Food and Drug Administration (FDA) 
3900 NCTR Road 
Jefferson, AR 72079 

Tel: 870-543-7538 
Fax: 870-543-7382 
Fax: hong.fang at fda.hhs.gov 

-----Original Message-----
From: henrik.bengtsson at gmail.com [mailto:henrik.bengtsson at gmail.com] On
Behalf Of Henrik Bengtsson
Sent: Monday, February 25, 2008 7:48 PM
To: Fang, Hong*
Cc: Murim Choi; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] RMA, d-chip and Plier for new chip type
Human/Mouse/Rat Gene

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>
> 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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