[BioC] HTqPCR rbind() function

[Michael Muratet]

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