Question: RUVseq for microRNAs
0
gravatar for sergio.espeso-gil
4.1 years ago by
New York
sergio.espeso-gil0 wrote:

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

 

microrna ruvseq ruv • 976 views
ADD COMMENTlink modified 4.0 years ago • written 4.1 years ago by sergio.espeso-gil0
Answer: RUVseq for microRNAs
0
gravatar for davide risso
4.1 years ago by
davide risso830
Weill Cornell Medicine
davide risso830 wrote:

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?

 

ADD COMMENTlink written 4.1 years ago by davide risso830

Hi David! I will, I am not now at the lab.  Next week I will post it. Thanks ! 

ADD REPLYlink written 4.1 years ago by sergio.espeso-gil0
Answer: RUVseq for microRNAs
0
gravatar for sergio.espeso-gil
4.0 years ago by
New York
sergio.espeso-gil0 wrote:

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. :-(

 


 

 

 

ADD COMMENTlink written 4.0 years ago by sergio.espeso-gil0
Answer: RUVseq for microRNAs
0
gravatar for sergio.espeso-gil
4.0 years ago by
New York
sergio.espeso-gil0 wrote:

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!

 

 

ADD COMMENTlink written 4.0 years ago by sergio.espeso-gil0

That's correct!

ADD REPLYlink written 4.0 years ago by davide risso830
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