Hi Heidi,


my question is how should be the format of the files.txt file, so that
HTqPCR can read in the information of the two different factors, should it
be like the example I wrote below? And what about the confidence intervals
to filter data, how does the package estimates them?
Cheers
Andreia

On Tue, Jan 26, 2010 at 10:23 PM, Heidi Dvinge <heidi@ebi.ac.uk> wrote:

> 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.
>
> HTH
> \Heidi
>
> > 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@fm.ul.pt
> >          andreia.fonseca@gmail.com
> >
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> >
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>
>
>


-- 
--------------------------------------------
Andreia J. Amaral
Unidade de Imunologia Clínica
Instituto de Medicina Molecular
Universidade de Lisboa
email: andreiaamaral@fm.ul.pt
         andreia.fonseca@gmail.com

	[[alternative HTML version deleted]]

