Hello,

I'm using the HTqPCR developed by Heidi Dvinge to perform some miRNA differential expression analysis from data obtained from TLDA arrays. 

I have 37 different data files (created by SDS), each one corresponding to a plate. Each file has the expression data of 24 different miRNAs (duplicated, so 48 features per sample) and each file contains the information of 8 samples.

I read the data with readCtData specifying n.features=48 and n.data=8, and the result is one object class qPCRset (presumably comprising the information of all the 37 data files). So far, so good, since I thought that specifying those parameters, the function would recognise separatedly to which sample belongs each feature.

However, reading the vignette I have got a little confused by section 12, which talks about using changeCtLayout function to split the data in the correct feature x samples. This section says that "Per default, readCtData reads each card into a qPCRset object as consisting of a single sample".

So, my question is, taking into account that my studied features are always in the same order, is it necessary that I use the changeCtLayout function, or is it enough with the readCtData specifying the number of samples per file?

Thanks in advanced, 

Ángela.