I am in a fix and want people out here to help me.
I have a control and treatment both in replicates so total 12 samples (including replicates). I have run the tophat pipeline (PS: I know i shouldn't have gone for it and should have chosen HISAT or any better pipeline). So after cuffdiff i got a file geneexp.diff that includes log2 fold change values. I set up the threshold cut off of +2 for upregulated and -2 for downregulated and p value less than 0.05
Now, how will i get a matrix to create heatmap ?? i have appx 2000 upregulated genes Do we need to take log2 fold change to create heatmap or fpkm values. my fpkm values range between 0.3 to 5000 is that wrong ?
my excel sheet is as follows test_id gene_id gene locus sample1 sample 2 value1 value 2 log2foldchange p value q value significance
post if you have any further queries.