[BioC] mas5calls now almost like affymetrix's

[James MacDonald]

The P, M, A calls from MAS5 don't (IMO) tell you whether the gene is
being expressed or not, but how well the PM signal can be distinguished
from the IM signal. Since rma doesn't use the MM or IM signal as an
estimator of non-specific binding, there is no way to make this call.

I think you could make a very strong case that you shouldn't actually
reject any measurements based on the expression values anyway. The gene
may not be expressed in some of your samples, but expressed at a very
low level in other samples. I would argue that these genes are likely
very interesting.

Also, the level of expression does not a priori give you an idea of the
phenotypic effect. In fact, for many genes I would imagine low
expression is all you ever get. For instance, gene expression in the
brain is extremely difficult to measure because the amount of mRNA
produced is so low.

It seems to me that most of the genes that are at the signal/noise
boundary are lost when you start doing statistical tests anyway, so
there is no profit in eliminating them beforehand.

Best,

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

>>> "Tom R. Fahland" <tfahland at genomatica.com> 02/06/04 11:58AM >>>
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.

-r

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