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
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
?cole Polytechnique F?d?rale de Lausanne (EPFL)
Institut de math?matiques
B?timent MA, Station 8 Tel: +41 21 693 2552
CH-1015 Lausanne Fax: +41 21 693 4303
SWITZERLAND
