Total count filter cutoff-edgeR

Question

[mahnazkiani]

Hello,

I'm using edgeR for analysis of may data and I'm not sure what total count filter value cutoff value I should use, My reads are paired 50bP reads and total reads per sample is about 80,000,000. I tried cutoff values of 5,10,15,30,50 and 100 and I only saw differences between 50 and 100 but still looking for logical reason to choose the cutoff value.

Appreciate your help,
Mahnaz

Answer 1

[Devon Ryan]

Just us the genefilter package and it'll allow you to determine the optimal threshold. I recommend reading the paper describing it as well as it gives the underlying justification.