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

[Henrik Bengtsson]

Hi,

there is currently no implementation/wrapper around the Plier
probe-level summarization model in aroma.affymetrix.  However, the
aroma.affymetrix framework has been designed so that it is fairly
straightforward to add wrappers to existing summarization methods, but
please note that it will take serious coding to do it.

Please address further questions specific to aroma.affymetrix to its
mailing list.

/Henrik

On Tue, Feb 26, 2008 at 7:03 AM, Fang, Hong* <hong.fang at fda.hhs.gov> wrote:
>  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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>
>