edgeR/DESeq2 error


I’ve been trying to perform differential expression of count data from HISAT2. I’ve tried both edgeR and DESeq2 and they both consistently result in the same error:

Fatal error: Exit code 1 ()
Error in library(methods, quietly = TRUE, warn.conflicts = FALSE) :
unused argument(s) (quietly = TRUE)

What does this mean??


what did you determined for your names of groups in deseq or edgeR ?


For edgeR, I manually entered factor information as follows:

Factor name: treatment
Groups: A,A,A,A,A,A,B,B,B,B,B,B,C,C,C,C,C,D,D,D,D,D

So there’s 4 treatments with 6 replicates of A and B, and 5 replicates of C and D.


i think its because the names of your groups. they shouldnt be same, and you cant use any letter exept alphabetic or numeric.