[BioC] Using HTqPCR for Fluidigm BioMark input data (48.48 array)

[Fletez-Brant, Christopher (NIH/VRC) [C]]

Jens,

If your qPCRset recognizes that there are 47 features and 3 samples, then
you should be able to perform downstream analyses.  If you are having
trouble modifying sample names, I have been storing sample names in a
file, ordered as the actual samples are in the Fluidigm output file, then
assigning sample names.  That is, something like:

Temp <- read.csv("sample.names.csv")
sampleNames(raw) <- Temp


Best,
Kipper

On 11/11/12 3:27 AM, "Jens Durruthy-Durruthy" <jensdd at stanford.edu> wrote:

>Hi all,
>
>I'm fairly new to the HTqPCR package and to R.
>I wanted to analyze my Ct values that I get from the BioMark output in
>form
>of a .cvs file. I managed to read my file in with:
>
>> raw<-readCtData(files="test2.csv",format="BioMark",n.features=47,
>+ n.data=3,samples=samples)
>Warning message:
>In readCtData(files = "test2.csv", format = "BioMark", n.features = 47,  :
>  Not enough sample names provided; using Sample1, Sample2, Š Instead
>
>> show(raw)
>An object of class "qPCRset"
>Size:  47 features, 3 samples
>Feature types:   
>Feature names:  HSP90AB1 CD13 COL1A1 ...
>Feature classes:  
>Feature categories:  OK
>Sample names:  Sample1 Sample2 Sample3 ...
>
>I ran 3 samples (three different cell types), each in 6 biological and 2
>technical replicates (12 total) but I don't know how to modify or edit my
>qPCRset object in order to visualize them or perform downstream analysis
>(PCA, clustering etc.). I read through the PDF "HTqPCR - high­throughput
>qPCR analysis in R and Bioconductor" by Heidi Dvinge but couldn't find an
>answer to my specific problem (mainly because I'm fairly new to the
>language
>R I think).
>
>If anyone could help out I would greatly appreciate it. Let me know if I
>need to provide additional information about the input .cvs file)
>
>Thanks!
>Jens
>
>:: Jens Durruthy-Durruthy ::
>:: Research Scholar ::
>:: Reijo Pera Lab ::
>
>:: Stanford University School of Medicine ::
>:: Institute for Stem Cell Biology & Regenerative Medicine ::
>:: Lorry Lokey Stem Cell Research Building ::
>:: 265 Campus Drive, Rm 3015 ::
>:: Stanford, CA 94305 € United States ::
>:: Mail: durruthy at stanford.edu ::
>:: Phone: +1-650-498-7303 ::
>:: Fax: 650-725-6910 ::
> 
>
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