[BioC] Limma and Affymetrix ?

Stan Smiley swsmiley at genetics.utah.edu
Wed Feb 11 23:39:31 MET 2004

I have been looking for some examples of limma with Affymetrix data. There
is a simple example in the documentation, but not a case study as with the
dye swap experiments, and I am confused as to how to proceed with using
limma on my data.

I need to eventually analyze a 2^4 factorial experiment, but I'd like to
start with a smaller example so I can get the idea first. I know what
contrasts are of interest to me, but I am unclear on how to use them with

ie. For a 2^3 factorial experiment:
3 Factors A,B,C ; each at two levels, high and low.

Treat		Factors
ments	A	B	C
c	low	low	low
a	high	low	low
b	low	high	low
c	low	low	high
ab	high	high	low
ac	high	low	high
bc    low	high	high
abc	high	high	high

If I'm thinking about this correctly, the seven effects I'm looking for
would be:

Single: For A,B or C alone
2x interactions: AB, AC and BC
3x interaction : ABC

With corresponding contrasts of:

4A   = -c + a - b + ab - c + ac - bc + abc
4B   = -c - a + b + ab - c - ac + bc + abc
4C   = -c - a - b - ab + c + ac + bc + abc

4AB  = +c - a - b + ab + c - ac - bc + abc
4AC  = +c - a + b - ab - c + ac - bc + abc
4BC  = +c + a - b - ab - c - ac + bc + abc

4ABC = -c + a + b - ab + c - ac - bc + abc

I'm unsure how to proceed in getting significant genes
from each contrast.

Any help and/or references to examples etc. would be greatly

Thanks for reading this far!

Stan Smiley
stan.smiley at genetics.utah.edu

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