Count Matrix normalisation for downstream analysis and for creating heatmap of targeted genes
Hello Everyone!
I have a count matrix generated from stringtie (from FPKM to readcount using prepDE.py3 of stringtie). i would like to create heatmap of targeted genes across samples.
My questions are :
1) Before creating heatmap do we need to normalize the read count data
2) If it is necessary , i was thinking of normalizing something like this, given gene-x and its read count across control, treatment1,treatment2 in trpilicates, ill calculate the average of all the read counts of gene-x across samples and then with that ill divide each read count by averaged read count and use that resulting value for plotting
is this right way to proceed ?
if you have any other methods please suggest.
Thank you!
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