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Daniel Brewer
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@daniel-brewer-1791
Last seen 9.7 years ago
Hi,
I have results from a series of 2-colour microarray experiements that
compare reference RNA to RNA from cells that fall into 4 catergories:
Cancer CD133+
Normal CD133+
Cancer CD133-
Normal CD133-
What I would like to find genes that are:
1) Significantly different from the reference RNA
AND
2) either (in both CD133+/- seperately)
i) significantly different between cancer and normal
or ii) significantly _similar_ between cancer and normal
I have been thinking of using the following strategy:
1) Treat CD133+ and - results separately
2) Use results from lmFit to filter out genes that are not
significantly
different from reference RNA in BOTH Cancer and normal
3) Perform a t-test between cancer and normal results and take genes
with p>0.05 as significantly different and p>0.95 as significantly
similar.
Is this a reasonable approach or would it be better to use ANOVA or
regression analysis. To add to the complexity at some point I would
also like to compare the CD133+/- samples
Many Thanks
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Daniel Brewer, Ph.D.
Institute of Cancer Research