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

[Fang, Hong*]

 Hi, Henrik:

Thanks for the information!

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


Best Regards,

Hong 

--------------------------------------------------------
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:

  http://www.braju.com/R/aroma.affymetrix/

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.

Cheers

/Henrik

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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