[BioC] HTqPCR rbind() function

[Heidi Dvinge]

Hello Michael,

I haven't tried working with data spanning multiple cards, but my $0.02 are:

- Combining files by hand (either pairwise or all together): Wouldn't be
my favourite method, since it involves manual work (*shudder*)
- Combining qPCRsets with rbind and cbind: Probably a better option, since
you don't necessarily want to normalise the two different types of ABI
cards together, but rather do it in two batches before combining them.
Depends on the data I guess.

Either way, if any of this fails in the downstream process, then feel free
to send your code + error messages to the list. Whatever bugs are creeping
around in HTqPCR, I need to fix them!

HTH
\Heidi

> Greetings
>
> I have just upgraded R to 2.11, Bioconductor to 2.6 and HTqPCR to 1.2.
>
> I am working with data from mouse miRNA experiments on the 7900HT
> using what I believe are stock ABI cards. Each experimental treatment
> consists of two distinct cards and there are four treatments for a
> total of four pairs. There are 4 common controls on each member of the
> pair (MammU6) but they are otherwise unique. All of the features on
> the first card are unique (except for the MammU6 control) and the
> second card has a couple of hundred features in duplicate and a four
> or so controls repeated four times.
>
> What would be the best way to create the qPCRset object? I have tried
> to concatenate the files by hand and read them in with read.delim and
> create the qPCRset object by hand. I have tried
> readCtData(...,SDS=TRUE,sample=c("sample_label")) and combined the two
> qPCRset objects with rbind() and four samples with cbind(). I have
> tried to read all the samples in one file. At some point, each one of
> these approaches fails in the downstream processing. Before I start
> posting error messages, I thought I would see if anyone has any
> recommendations.
>
> Any suggestions will be welcomed.
>
> Thanks
>
> Mike
>
>
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet at hudsonalpha.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
>
>
>
>
>