[BioC] Tiling array application

[James MacDonald]

It doesn't make any sense to use gcrma() if you don't have MM probes;
the idea behind gcrma is to come up with a better measure of background
than the MM measure itself. A modification of gcrma() that doesn't use
MM probes is rma().

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
>>> Shinhan Shiu <shiu at uchicago.edu> 04/01/05 5:13 PM >>>
We are trying to use GCRMA to adjust raw intensity values from tiling
chip 
experiments (Arabidopsis). But the affy Arabidopsis tiling chip do not
have 
mismatch probes and it seems the mismatch probe intensity is absolutely 
required in:

bg.parameters.ns

Where the mismatch probe intensities, mismatch probe affinity, and
perfect 
match probe affinities are passed. I wonder how this function can be 
modified so only perfect match probe info is used. Thanks.

Shinhan


********************************
  Shinhan Shiu
  Dept. of Ecology and Evolution
  University of Chicago

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