Re: HTqPCR

Hi Simon,

thanks for your email, and sorry if the example files are shoddy. I'm
travelling the next couple of days, but will have a look as soon as I'm
back.

Off the top of my head, I seem to remember that for some of the BioMark
files I originally had access to, the sample names were in slightly
different formats. Therefore, as a temporary measure I just ignored sample
names in the file, in which case the sample names can be added with the
'samples' parameter to readCtData(). Or alternative, added with
sampleNames(object) <- c("",...) later. Obviously, that's not optimal
though, and I should fix that for future versions.

In the case of the example file, a (somewhat messy) workaround may be to say:

> exPath <- system.file("exData", package = "HTqPCR")
> temp	<- read.csv(file.path(exPath, "BioMark_sample.csv"), as.is=TRUE,
skip=11)
> raw1 <- readCtData(files = "BioMark_sample.csv", path = exPath, format =
"BioMark", n.features = 48, n.data = 48,
samples=temp$Name[seq(1,nrow(temp), 48)])
> head(sampleNames(raw1))
[1] "no preamp"     "preamp neat"   "no preamp.1"   "preamp neat.1" "no
preamp.2"
[6] "preamp neat.2"

Apart from the missing sample names, that what exactly are the problems
you're seeing in importing your own data into a qPCRset object?