[BioC] DESeq without replicates, Problem trying to obtain significant hits

Simon Anders anders at embl.de
Wed Mar 14 16:30:12 CET 2012

Hi Melissa

On 03/14/2012 03:50 PM, Melissa.Martin at lshtm.ac.uk wrote:
> I am trying to use the DEseq package without replicates. When I look for significant hits all of them are False. Could this be a real result? Below are the commands that I enter.

Yes, it is entirely plausible that this is a correct result. Remember 
that the "blind" mode is just a function to attempt to rescue a botched 
experimental design and get at least a few hits out of it. Whether this 
works or not depends on the nature of the data. As you did not tell us 
much about what kind of biology you are looking at, this is hard to say.


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