[BioC] HTqPCR - limmaCtData using samples with different number of replicates?

[Heidi Dvinge]

Hi Kipper,

> Dear List,
>
> I am using HTqPCR to analyze Fluidigm data (specifically, the 96*96
> format).  I have been using specifically limmaCtData to look for
> differential expression between groups, always having the same number of
> replicates.  However, I currently have a dataset of several groups with 3
> replicates and 1 group with  2 replicates.  As far as I can tell,
> limmaCtData expects the number of replicates to be the same between groups
> (i.e. there is only one 'ndups' parameter).  Has anyone else encountered
> this issue?
>
ndups actually refers to the number of replicate *features*, i.e. genes,
on your plate. As long as you use the same platform for all your samples,
this should be constant.

The number of samples within each group is indicated using the design
matrix in limmaCtData, and the parameter 'groups' in ttestCtData. So in
limmaCtData you can just use a design matrix along the lines of:

> samples <- rep(c("treat1", "treat2", "treat3", "control"), c(3,2,3,3))
> design <- model.matrix(~0+samples)

You then indicate your comparisons of interest in the contrast matrix, and
use both matrices in your call to limmaCtData.

If I've misunderstood you and you actually have a variable number of
replicates of each gene, then I'm afraid limmaCtData isn't capable of
handling this with ndups.

HTH
\Heidi

> Thank you,
> Kipper Fletez-Brant
>
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