differential gene expression analysis

Question

[mohamedelshaer66]

if i have a 183 columns representing 183 patients, genes are represented in rows. how to remove genes that have zero reads in 25% of the patients.

Answer 1

[rpolicastro]

I'm assuming you are doing this in R because of the popularity of DESeq2 and edgeR.

patient_data <- patient_data[rowSums(patient_data == 0) < (ncol(patient_data) * 0.25), ]