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@stanford.edu ::
:: Phone: +1-650-498-7303 ::
:: Fax: 650-725-6910 ::
 

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