[BioC] Limma: Design matrix question

[Daniel Brewer]

Hi,

I have an experiment where I have two different siRNAs (a and b) that
target the same gene.  I have 18 two colour microarray experiments where
the control on Cy3 is siRNA non-targetting.  For each siRNA there is
three time points and for each of those time points three replicates
(biological).  I am planning on ignoring the time point for now.  The
comparisons I would like to make are siRNA a vs control, siRNA b vs
control, both siRNA vs control and a vs b.

So this is the design matrix I have got set up:

      a b siRNA
1a_48 1 0     1
1a_72 1 0     1
1a_96 1 0     1
1b_48 0 1     1
1b_72 0 1     1
1b_96 0 1     1
2a_48 1 0     1
2a_72 1 0     1
2a_96 1 0     1
2b_48 0 1     1
2b_72 0 1     1
2b_96 0 1     1
3a_48 1 0     1
3a_72 1 0     1
3a_96 1 0     1
3b_48 0 1     1
3b_72 0 1     1
3b_96 0 1     1

I think I must be doing something wrong as when I run the lmFit()
function I get the following:

> fit <- lmFit(MA, design)
Coefficients not estimable: siRNA
Warning message:
In lmFit(MA, design) :
  Some coefficients not estimable: coefficient interpretation may vary.

Is my design matrix incorrect?

Thanks

-- 
**************************************************************
Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk
**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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