[BioC] HTqPCR and factorial design

Heidi Dvinge heidi at ebi.ac.uk
Tue Jan 26 23:23:16 CET 2010

Hello Andreia,

actually, HTqPCR can handle multi-factor design, there's just no example
of that in the vignette (will consider adding it in the next revision).

The function limmaCtData takes all the arguments that you'd use if you
were analysing microarray data using lmFit and contrasts.fit from the
limma package.  You need to specify the design and contrast matrix
yourself though. As I recall, the limma user's guide has a couple of
example involving factorial design.


> Dear list,
> Soon I will receive data from the qpcr Exicon platform to analyze and I
> have
> been playing around with HTqPCR package, however from the vignete, it
> seems
> that is only capable of deleting with data design of one factor, how do I
> handle it with a factorial design, namely how do I read the data and
> create
> the model.matrix, the examples only consider one factor. Another question
> is
> concerning part 5 of the vignete, how are the Confidence values estimated?
> is is based in the variance of the data?
> In order for you to understand my doubts here is my design is a 2x3
> design,
> I don't have replicates, but each file has the CT values for each gene
> frome
> pooled RNA of 10 patients.
>             factor1   factor2
> file1.txt  NS        C
> file2.txt  NS        H1
> file3.txt  NS        H2
> file4.txt    S        C
> file5.txt    S        H1
> file6.txt    S        H2
> Thanks for your help.
> with kind regards,
> Andreia
> --
> --------------------------------------------
> Andreia J. Amaral
> Unidade de Imunologia Clínica
> Instituto de Medicina Molecular
> Universidade de Lisboa
> email: andreiaamaral at fm.ul.pt
>          andreia.fonseca at gmail.com
> 	[[alternative HTML version deleted]]
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