I'm having some trouble modifying my qPCR plate layout to be compatible with the R package HTqPCR. Please let me know if you have any suggestions.

Unlike the example in the vignette, I have a "low throughput" plate, coming off of the ABI Viia 7 qPCR machine. I have 3 features (genes) and 5 samples in technical replicate.  I'm able to import my SDS txt file with a modified readCtData: 

myqPCRset <- readCtData(files = "data.txt", path = mypath, format = "SDS", column.info = list(feature=5, position=2,Ct=9), n.features = 3, n.data = 10)

I added replicate details in pData (as in the vignette example):

pData(myqPCRset) <- data.frame((Names = samplenames), Replicate = rep(1:2,5))

Looking at chapter 12 in the vignette regarding multiple samples per plate, I tried to changeCtLayout, but keep running in to an error.

grpnames <- rep(as.character(unique(data$Sample.Name)), each = 2)

sample5.order <- rep(c(grpnames), each = 3)

Which gives: 

[1] "A" "A" "A" "A" "A"

[6] "A" "B" "B" "B" "B"

[11] "B" "B"  ........

etc.

I run in to this error:

myqPCRset.new5 <- changeCtLayout(data, sample.order = sample5.order)

Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘exprs’ for signature ‘"data.frame"’

What's going wrong?