[BioC] HTqPCR package

[Heidi Dvinge]

Hello Patrick,

sorry for the delay in replying.

> Dear Heidi,
>
> I just found out about your R-package for analyzing PCR data. I started to
> read about it but suffered with a silly problem.
> My output files look like the ones attached: 1 per sample and 3 technical
> replicate per file and used the following:
>
> files <- read.delim(file.path(path, "file listing.txt"))
> raw <- readCtData(files=files$File, path=path,
> n.features=48,feature=1,Ct=2,header=FALSE, SDS=FALSE)
>
> The readCtData command did not work. Could you give some assistance to a
> non-frequent user of R?
>
In case this is still relevant, then the issue is that your file doesn't
contain a lot of the standard high-throughput qPCR information, such as
well position on a plate, and type of probe (control or 'real').
Therefore, you need to set these input to NULL. For examplke, this should
work:

> files	<- read.delim("file listing.txt", as.is=TRUE)
> raw	<- readCtData(files=files$File, flag=NULL, feature=1, type=NULL,
position=NULL, Ct=2, n.features=48)
Warning message:
In readCtData(files = files$File, flag = NULL, feature = 1, type = NULL,  :
  One or more samples contain NAs. Consider replacing these with e.g.
Ct=40 now.
> show(raw)
An object of class "qPCRset"
Size:  48 features, 3 samples
Feature types:		 Target
Feature names:		 Hprt1 B2m Gapdh ...
Feature classes:
Feature categories:	 OK
Sample names:		 31H 34H 35H ...

You can now continue as outlined in the vignette, and for example check
the distribution of your Ct values:

> plotCtBoxes(raw)
> plotCtPairs(raw)

Note the warning about missing values. You can keep those as NA if you
prefer, but if you want to replace them you can say e.g.

> exprs(raw)[is.na(exprs(raw))] <- 40


HTH
\Heidi


> Thank you so much.
>
> Best wishes,
>
> Patrick
>
>
> Patrick De Boever, PhD, MSc
> Flemish Institute for Technological Research (VITO)
> Unit Environmental Risk and Health
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