[BioC] Fwd: Re: Scaling Factor for Affymetrix chips.

[Naomi Altman]

>To: "Khan, Sohail" <khan at cshl.edu>
>From: Naomi Altman <naomi at stat.psu.edu>
>Subject: Re: [BioC] Scaling Factor for  Affymetrix chips.
>Cc:
>Bcc:
>X-Eudora-Signature: <work>
>Date: Sun, 12 Mar 2006 16:10:37 -0500
>
>Personally, usually go straight to the probe level data and do:
>
>1) image plot of all the arrays
>2) pairs plot of all pm probes on all pairs of arrays (preferably 
>using hexbin)
>3) density or histogram of all pm probes on each array
>4) RNA degradation plot  (looking for parallel lines)
>
>--Naomi
>
>
>At 11:49 AM 3/12/2006, you wrote:
>>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
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>Naomi S. Altman                                814-865-3791 (voice)
>Associate Professor
>Dept. of Statistics                              814-863-7114 (fax)
>Penn State University                         814-865-1348 (Statistics)
>University Park, PA 16802-2111

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111