[BioC] HTqPCR problem with creation of qPCRset

[Elisabeth Gilis]

Hi,

I'm a PhD student from the University of Ghent, and I'm just starting  
to learn how to work with R.
The initial aim is to analyse qPCR data with the package HTqPCR so I  
read quite a few manuals regarding the program R and HTqPCR.
My problem is situated right at the beginning of the analysis, namely  
loading my data.
I think I got it correctly that I first have to make a so-called  
"qPCRset" of my data?
So just to begin easily, I made an Excel file with just 3 columns:
Sample    Name      Cp
A1        Actin     17
A2        Actin     18
A3        Actin     16

And saved it as a text file "test.qPCR.txt" to be able to import it.
For this I downloaded "RStudio" and in this program I imported my  
dataset "test.qPCR.txt.
(This is what is printed on the command line (not by me, but by the  
program RStudio):
> test.qPCR <- read.delim("~/test.qPCR.txt", dec=",")

This was no problem at all, I actually get a nice data frame (when I  
type the command >class(test.qPCR)
I get [1]"data.frame").
Then I loaded the package HTqPCR and at this point I'm stuck.
I want to use my dataset that I imported to make a qPCRset, but I have  
no clue how to do it.
I tried already some some commands, but they all give me errors, for example:

> raw<-readCtData("test.qPCR.txt")
Error in `[.data.frame`(sample, , column.info[["Ct"]]) :
   undefined columns selected
In addition: Warning message:
In .readCtPlain(readfile = readfile, header = header, n.features =  
n.features,  :
   384 gene names (rows) expected, got 4


> raw<-readCtData(test.qPCR)
Error in read.table(file = file, header = header, sep = sep, quote = quote,  :
   'file' must be a character string or connection


> raw<-readCtData(files:"test.qPCR",path=path,format="plain")
Error in files:"test.qPCR" : NA/NaN argument
In addition: Warning messages:
1: In files:"test.qPCR" :
   numerical expression has 2 elements: only the first used
2: In readCtData(files:"test.qPCR", path = path, format = "plain") :
   NAs introduced by coercion

So I'm really stuck here, if somebody would help me to get started, I  
would be really grateful!
Kind regards,
Elisabeth Gilis, PhD student
Department of Rheumatology
Ghent University