[BioC] RMA and GeneCluster

[James MacDonald]

Assuming that GeneCluster makes a 'heatmap' like Eisen's software, you
will probably have to normalize the data using GeneCluster, for two
reasons.

1.) In order for the data to be visualized as being up or down
regulated, they have to be distributed around zero. Down regulated genes
will have negative expression values and up regulated genes will have
positive values.

2.) If GeneCluster is similar to Eisen's cluster, the range for the
colors is (-3, 3), where -3 is as dark a green as you will get and 3 is
as bright a red. Any values outside this range will not be
distinguishable. 

Therefore, data are usually mean (or median) centered (e.g., mean=0),
and the variance adjusted to 1.

However, I am making a BIG assumption that GeneCluster is similar to
Eisen's Cluster. If I am wrong, my apologies in advance. ;-D

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

>>> "Huang, Mingqian " <MHUANG1 at partners.org> 10/15/03 12:10PM >>>
Hi,

I'm trying to use GeneCluster to analyze our GeneChip data normalized
with RMA.
However, there is another normalization option in GeneCluster:

Normalize to Mean ____ and Variance ____

The results I got with or without this step are quite different, even
though the
data has been treated with RMA. What does this normalization process
do? Should
I do this step + RMA or should I just rely on RMA?

Thanks for your help.

Mingqian Huang

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