I have silly questions, I checked edgeR user's guide and I didn't find any answer to my question.
I have two different samples. I want to compare with each other and find differential expressions.
So, I run this code :
y1 <- estimateCommonDisp(y, verbose = TRUE) and it gave me this message :
Warning message: In estimateCommonDisp.DGEList(y, verbose = TRUE) : There is no replication, setting dispersion to NA.
I get the same warning when I use estimateDisp() and estimateTagwiseDisp() functions.
What does it mean 'there is no replication' because I already have two samples, how can I create the replication?
Do you have any suggestion to find the differential expression for two samples?
Thank you all!
Hi, If you have no replicate for your samples, then you can also use NOISeq package. The Pairwise Differential Expression Analysis (Without Replicates) functionality offers a strategy for analyzing RNA-seq datasets that do not have replicates. It is based on the software package NOISeq, which belongs to the Bioconductor project. NOISeq is a novel nonparametric approach for the identification for differentially expressed genes from RNA-Seq count data.