[BioC] Finding similarities and differences for more than one catergory

[Daniel Brewer]

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

-- 
**************************************************************

Daniel Brewer, Ph.D.

Institute of Cancer Research