I have one csv file that contains the delta Ct values for several samples (columns) and genes as row names. I have samples from different Groups, Grp A, Grp B and Grp C. My data columns look something like this. Samples in Group A and B start with baseline disease condition while Group C samples are healthy.
Gene GrpA1_baseline GrpA1_flare GrpA2_baseline GrpA2_flare GrpB1_baseline GrpB2_baseline GrpC1.1_healthy GrpC1.2_healthy GrpC2.1_healthy GrpC2.2_healthy
I have different conditions within Group A biological replicates (meaning samples), only baseline condition for Group B biological replicates, and I have 2 technical replicates for each sample in Group C. I was wondering how I could create a new qPCRset object using HTqPCR package in R. I understand that I could use the readCtData function but I am unsure of how to specify and tackle biological replicates and technical replicates or how to read all this in from one file.
The ultimate goal is for me to find differentially expressed genes between different groups (GrpA_flare vs GrpC_healthy) for example. As I am completely new to analyzing Ct values, any advice at all about how I could go about doing this would be greatly appreciated. Thank you.