[BioC] Scaling Factor for Affymetrix chips.

[Darlene Goldstein]

Khan, Sohail <khan at ...> writes:

> 
> Dear All,
> 
> Is the Scaling Factor (from GCOS) still neccessary for the quality assessment
of Affy, eventhough we are
> applying RMA or GCRMA for the probe level analysis??  Many times we only have
the .cel files from an
> experiment, in this case how can one have a look at the SF using any BioC
package?  Could you recommend a
> comprehensive QC method/procedure for the Affymetrix chip? Thanks.
> 
> Sohail Khan 
> Scientific Programmer 
> COLD SPRING HARBOR LABORATORY 
> Genome Research Center 
> 500 Sunnyside Boulevard 
> Woodbury, NY 11797 
> (516)422-4076
> 

Hi - have a look at the package affyPLM and its vignette on quality assessment.

Best regards, 

Darlene

-- 
Darlene Goldstein
École Polytechnique Fédérale de Lausanne (EPFL)
Institut de mathématiques
Bâtiment MA, Station 8        Tel: +41 21 693 2552
CH-1015 Lausanne              Fax: +41 21 693 4303
SWITZERLAND