Hello,

I’m user of Bio-Rad qPCR systems. I export the data obtained from Bio-Rad software to csv format, a sample is attached to the next WeTransfer link: https://we.tl/t-9ZzBkVAkEo.

Then, in order to create a qPCRset object I follow the section 13 of the
HTqPCR User Manual, through the next R code:

path = "C://TextesD//UdL//QuartFPU//qPCRStatistics"
raw <- readCtData(files = "data.csv", path = path,format = "CFX",
n.features = 1,n.data = 35)

The qPCRset object is created without errors.

However, when I execute the following command in the R terminal:

> raw@assayData$exprs

It displays:
​
Sample1  Sample2  Sample3  Sample4  Sample5  Sample6  Sample7  Sample8
Sample9 Sample10 Sample11 Sample12 Sample13 Sample14
1 23.69529 23.69529 21.29344 21.29344 21.83142 21.83142 21.80268 21.80268
21.8967  21.8967 22.09014 22.09014 20.82197 20.82197

As it can see, Ct values are repeated in groups of 2.  Therefore, this
error is caused by that the R package are taking into account Cq mean
value in csv file as Ct instead of Cq value.

Then, maybe is better to create tab delimited file or csv file by hand?
However, which and how columns I need to indicate in order to create a
qPCRset object successfully without obtaining the following error message:

Error in `[.data.frame`(sample, , column.info[["Ct"]]) :
  undefined columns selected

I really appreciate your help because I'm not capable to create a tab delimited file to overcome the error indicated above.

Thanks a lot for your help,

David Bars

PhD Student

University of Lleida