I have around 1200 samples as columns and 60,000 genes with Htseq-Counts data. Before normalization with voom function I want to do filtering step.

I want to remove genes whose expression is == 0 in at least 10 samples.

Can I do this with read counts itself or should I transform counts to cpm?

If filtering with counts data is fine May I know how to do this.

Thank you !!

I have around 1200 samples as columns and 60,000 genes with Htseq-Counts data. Before normalization with voom function I want to do filtering step.

I want to remove genes whose expression is == 0 in at least 10 samples.

Can I do this with read counts itself or should I transform counts to cpm?

If filtering with counts data is fine May I know how to do this.