I came across this package and based on the reference material it seems pretty straight forward and helpful.

http://www.ebi.ac.uk/sites/ebi.ac.uk/files/groups/bertone/software/HTqPCR.pdf
http://bioinformatics.oxfordjournals.org/content/25/24/3325.full.pdf

However, Im relatively new to R and Bioconductor so I am getting stuck at the beginning...

I have a different data format, a matrix of 63 genes (columns) and 12 samples (raws) with Ct values, already averaged over the technical repeats.

I also have a header indicating the gene names (so i set header=true).

I load my text tab separated matrix with read.delim and then i use readCtData like this:

raw <- readCtData(files = files$File, path = path, header=true, format="plain", n.features=756, n.data=63, sample)

where :

> sa<-c("s1", "s2", "s3", "s4", "s5", "s6", "s7", "s8", "s9", "s10", "s11", "s12")
> sample=sa

I get the following error:
Error in data.frame(sample = 1:length(samples), row.names = samples) : 
  row names supplied are of the wrong length

1. What could be the issue?

2. How do i import this matrix, including the gene names in the header?

Hope the creator can support me or any of the users of the HTqPCR package.

Thanks

/Virginia

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] tools     parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
[1] HTqPCR_1.20.0        limma_3.22.7         RColorBrewer_1.1-2   Biobase_2.26.0      
[5] BiocGenerics_0.12.1  BiocInstaller_1.16.5

loaded via a namespace (and not attached):
 [1] affy_1.44.0           affyio_1.34.0         bitops_1.0-6          caTools_1.17.1       
 [5] gdata_2.16.1          gplots_2.17.0         gtools_3.4.2          KernSmooth_2.23-14   
 [9] preprocessCore_1.28.0 stats4_3.1.1          zlibbioc_1.12.0