Count Matrix normalisation for downstream analysis and for creating heatmap of targeted genes

Count Matrix normalisation for downstream analysis and for creating heatmap of targeted genes

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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!


stringtie


statistics


normalisation


transcriptomicanalysis


countmatrix

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