Hi

Section 20.5 of the limma userguide describes how to analyse a 2x2
factorial design using 2 colour microarrays.  There are two factors,
time (p11 and p21) and mouse (wt and mu).  This results in 4 different
RNA classes, p11.wt, p11.mt, p21.wt and p21.mt and the interaction term
is calculated as

(p21.mt - p11.mt) - (p11.mt - p11.wt)

(NB is the above a typo?  "p11.mt" appears twice....)

Anyway, I have a 3x2 factorial experiment; infection (gal, typ and
uninfected) and bird (6, 15).  This results in 6 RNA classes: 6Stm,
15Stm, 6Gal, 15Gal, 6Uninf, 15Uninf.  They are not compared using a
common reference, more a double loop design where one side of the loop
is shared, eg:

6Stm  - 6Uinf  - 6Gal
  |        |       |
15Stm - 15Uinf - 15Gal 

(view the above in courier font and it will make sense)

So my question is, how do I calculate the interaction term for this
experiment in the contrasts matrix?

Many thanks

Mick


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