Dear heidi,
thank you for your reply. The datasets come  from a 96 well qPCR plate, but
only 80 reactions have good quality. Each line corresponds to a separate
plate, with the same probes. I would like to compare A and B. Thanks for
your help.
Kind regards,
Andreia

On Sat, Apr 24, 2010 at 12:45 PM, Heidi Dvinge <heidi@ebi.ac.uk> wrote:

> Hello Andreia,
>
> hm, slightly tricky. Are these data sets from some sort of commercial
> platform, like the ABI TLDA cards, or from normal qPCR reactions on a 384
> well plate or similar? Just to make sure I understand you experiment
> right, do you have something like this?
>
> Sample  Cell_type Platform RT_reaction
> ------------------------------------
> 1   A    type1    RT1
> 1   A    type1    RT1
> 1   A    type2    RT2
> 2   A    type2    RT1
> 2   B    type2    RT1
> 3   B    type2    RT1
> 4   B    type2    RT1
>
> Is each line a separate plate? Or would the "Platform" column correspond
> to 2 individual plates, where multiple samples can be loaded onto each
> plate?
> What exactly is your primary interest here? Difference between cell types
> A and B? I think we need some specification here, for us to help you
> properly.
>
> If you have different kinds of plates, then you could potentially include
> pate as a batch effect when doing your analysis. This will require you to
> use limmaCtData() for your test. This is based on the function lmFit from
> the limma package, which has some nice examples of how to take this sort
> of information into account. Although it looks like you have too many
> variables here to consider all of them.
>
> By the way, you don't necessarily need one file per sample. As long as you
> have the sample number of genes per sample, e.g. 384, then with HTqPCR
> version 1.2.0 you can use the n.data parameter in readCtData() to indicate
> how many sets of data are in each file.
>
> HTH
> \Heidi
>
> > Dear Heidi,
> >
> > I have received a data set from a qPCR miRNA set where I have
> >
> > sample1 - 2 replicates from the same RT reaction
> >                1 replicate from an independen RT reaction     cell_type:A
> > sample 2 - cell type : A
> > sample2 cell_type:B
> > sample3 cell_type:B
> > sample 4 cell_type:B
> >
> > I saw that I should prepare one file per sample, but the replicates of
> > sample1 have been produced in different plates and one is even from
> > another
> > RT reaction. How can I account for this using your package?
> > Thanks in advacne for your reply.
> > 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
> >
>
>
>


-- 
--------------------------------------------
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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