How to perform TMM normalization for my miRNA data

Question

[k.kathirvel93]

Hi Everyone,

I am new to R. am doing miRNA_seq data analysis with three different tissues. I need to normalize my datas by TMM. So can any one help me 1. How to do TMM ( suggest me some R code) 2. How my Input count file should looks like for TMM. Thanks in advance,

Answer 1

[h.mon]

I will suggest you a lot of code, found at edgeR Users Guide. Although there is no miRNA example, if you have mapped your reads and then summarized read counts mapping to each gene, then you can follow edgeR workflows found at the guide. The function calcNormFactors() will perform TMM normalization.

You input counts file should be in the form of integer counts, one gene per line. How did you perform the counts?

[k.kathirvel93]

Thanks h.mon am using FeatureCounts for quantification.