[BioC] Affy Question

[James MacDonald]

Some of the affy functions use the MM values and some do not. AFAIK, RMA
and playerout do not use MM values, whereas you can use either PM or
PM-MM for li.wong, and of course MAS and avgdiff use MM values.

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> Jason Skelton <jps at sanger.ac.uk> 10/22/03 11:30AM >>>
Hi

I'm not particulary familiar with any of the affy functions in 
bioconductor i'm under the impression that all of the affy functions
are 
based on using PM & MM values for any analysis.....

BUT

The Custom affy chip we have doesn't have Mismatches
I'd like to use Bioconductor only using the PM values from the CEL
file
& was wondering if this is possible at all in bioconductor...

If so can some suggest what functions need to be used


We can extract seperately
Normalised expression values
Background
No of probes
Gene Names
P-Values

but would prefer to be able to use the CEL file directly
and preferably the raw data

Cheers

Jason

-- 
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919

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