[R] filter high-throughput microarray data with noise

From: Weiwei Shi <helprhelp_at_gmail.com>
Date: Mon 11 Sep 2006 - 16:11:25 GMT

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.

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Received on Tue Sep 12 02:16:34 2006

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