Differential Analysis with EdgeR



gravatar for mlai2567

12 hours ago by


Hi all,

I’m trying to analyze an RNA-seq dataset that was just run. It consists of 3 conditions (Control, Treatment 1, Treatment 2) with 2 biological replicates (Cell line #1, Cell line #2) each. However, because the biological replicates are from cell lines of different passage number, there is variation in the base level of gene expression, even within the controls, making it difficult to conduct differential expression analysis across the replicates. For example, the expression value for the control of Cell line #1 may 1, but the control of cell line #2 may be 2. Thus, the expression values of the 2 treatments will vary accordingly, making it difficult to conduct edgeR analysis as there are a low number of differentially expressed genes with a FDR<0.05.

Because of this, I’m trying to measure the differential expression within each cell line individually. Is there a way with Galaxy EdgeR to:

  1. Measure differential expression with data that has no replicates?
  2. Is there a way to measure only fold change (and not FDR/p-value) on edgeR with Galaxy?
  3. I’ve tried inputting the data as replicates and have received abnormal logFC values of -200 to -300 with edgeR on Galaxy? Does anyone know why this might be the case?

Thanks in advance.

Cheers, Michael