Hello, all.

I am an undergraduate researcher who has recently begun the project of
analyzing some new microarray data.  I'm coming here after a large amount of
frustration and lack of finding any mention of how to solve my problem on
the mailing list.

I have a factorial design, with a targets matrix as below:

FileName Strain Cy5 Cy3
 1  File1 S I U
 2  File2 R I U
 3  File3 S I U
 4  File4 R I U
 5  File5 R I U
 6  File6 S I U
 7  File7 R I U
 8  File8 R I U
 9  File9 S I U
10 File10 S I U
11 File11 S U I
12 File12 S U I
13 File13 R U I
14 File14 R U I

Where R/S represent resistant and susceptible strains of the plant I am
studying, and I/U represent innoculation or lack thereof of a toxin that I
am testing for an effect of.

Values 11-14 are dye swap rows.

The kind of contrasts that I would like to be able to make are of the form:

(I.S - U.S)
(I.R - U.R)
(I.R-U.R) - (I.S-U.S)

However, the closest I have gotten using the user guide is something along
the lines of "I.U.S", "I.U.R",... etc.

This will not work because it doesn't take into account the dye swap, among
other problems.

Do you guys have any suggestions?  They would be very appreciated.

Thanks!

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