[R] filter high-throughput microarray data with noise

Weiwei Shi helprhelp at gmail.com
Mon Sep 11 18:11:25 CEST 2006

Dear Listers:

Currently I am doing a research using a microarray data. I have two
questions and hope I can get some help from here:

1. I have a dataset like the following, in which V1 is geneid,
v3...are the fold changes of expression levels for different patients.
There are multiple probes for one gene, so there are multiple rows.
You can see from column V11 and V13, the fold changes are very
different. Is it very common in microarray data analysis? Generally
how to deal with that? I don't want to use a p-value or something like
threshold to discretize them in this step yet.

           V1        V3             V5              V7        V9
     V11        V13
-2147022884  3.967828  5.010724  3.356568  1.227882   1.481481   1.870871
-2147022884 -4.031250 -1.441341 -1.036145 -3.583333  -8.953125  -3.201117
-2147022884 -2.016835 -1.568063 -1.079279 -1.288172 -50.875421 -39.554974

here is the variance
> x2.var[2,]
      Group.1       V3       V5       V7       V9      V11      V13
-2147022884 17.30989 14.15427 6.495755 5.791014 767.9342 510.5714

2. Is there any good reference on this kind of things? like online
materials or book.

Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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