Hi, has any of you used RUVseq to remove batch effects on microRNA data? 

I did with RUVs and RURr and seems to work. I had an error with RUVg, I need to figure out how to solve it

> set2<- RUVg(set, empirical, k=1 )

Error in svd(Ycenter[, cIdx]) : a dimension is zero

Hi Sergio,

are you sure that all the genes in "empirical" are in "set"? Can you please post the "head" of your expression matrix as well as your list of negative controls?

Hi Davide , sorry I have been quite busy. 

I understand now better the problem. I don't have a set of control genes, I am following the procedure of finding "in-silico empirical" negative controls, but in the first-pass DE analysis I am not finding any DE microRNA. See:

> summary(dt_empirical<-decideTestsDGE(lrt_empirical))

   [,1]

-1    0

0   808

1     0

Quite bad. :-(

I have another question Davide, maybe too naive, but I need it just to confirm. I am a bit confused with the direction of the contrast while using the tool, I am reading edgeR user guide and I am not fully sure, when you are specifying coef=2 in your example (let<-glmLRT(fit, coef=2)) you are doing Treatment against Control, right? Meaning that if logFC is negative you will have a increased gene expression in treatment and if it is positive the other way around...?

Thanks!