I am having one basic doubt.
I did my gene expression analysis using Illumina platform and data was analyzed in limma which gives me normalized and background substracted intensities,converted to log scale(log 2 intensities values)for both my control group and test group.I could identify DEG(differentially expressed genes) amongst the groups,suppose around 3000 genes.For identifying these genes the software groups my all test sample in 1 group and all control samples in 1 group and find a significant p value.When I go to generate the heat map ,mostly Fold changes values are used per sample.
Now do I have to calculate individual FC for every sample for generating heat map or does limma directly calculates FC
for plotting the heat map.?