[BioC] Testing for no change in RNA-seq data?

Ryan C. Thompson rct at thompsonclan.org
Thu Mar 21 01:05:32 CET 2013

Hi all,

So, we have several great packages for testing for evidence of 
differential expression using RNA-seq counts, and I am happily using 
those. However, I would like to know if there is any method for testing 
for evidence of equivalent expression. That is, I would like to show 
with some level of confidence that treatment X has no (or negligible) 
effect on gene Y. Is there any way to conduct such a test?

I know I can test for differential expression and see if the gene list 
comes up empty, but lack of evidence for differential expression is not 
the same as evidence for equivalent expression. So, are there any 
packages for doing equivalence testing on gene expression data? If it 
exists for limma, then I'm happy to run my data through voom to analyze 
it if necessary.


-Ryan Thompson

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