[BioC] mas5calls now almost like affymetrix's

Tom R. Fahland tfahland at genomatica.com
Fri Feb 6 17:58:44 MET 2004

I had a question relating to comparing a couple different normalizations
(like mas5 vs rma). If I used the default affy software, it produces
P,M,A values for each 
(as does mas5value call) expression measurement. But what is a good
method to reject measurements after rma is called since that doesn't
produce the P,M,A values? What do people genrally do?

Tom Fahland

-----Original Message-----
From: Rafael A. Irizarry [mailto:ririzarr at jhsph.edu] 
Sent: Thursday, February 05, 2004 21:42
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] mas5calls now almost like affymetrix's

Dear all,

Thanks to Mike Kuziora (Genelogic) the mas5calls function in affy now
gives results almost identical to Affymetrix MAS 5.0. This is in the
latest release 1.3.28

Thanks to Crispin Miller the devel pacakge of affy 1.4.13 has a version
of the mas5calls that works much faster. the results are almost
identical to those in 1.3.28.


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