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

[Fletez-Brant, Christopher (NIH/VRC) [C]]

Hi Heidi,

Thanks for setting me straight - I in fact have a panel of 96 unrepeated
features, used to produce experiments with a variable number of replicates
per group.  This works very well.

Thanks!

On 6/26/12 12:14 PM, "Heidi Dvinge" <heidi at ebi.ac.uk> wrote:

>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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>