[BioC] htqPCR question

[Heidi Dvinge]

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 at fm.ul.pt
>          andreia.fonseca at gmail.com
>