Simona, 

Yes, these sample and miRNA sizes look great. My greatest concern was due to the discrete nature of sequencing data as well as the potentially small number of miRNAs in a given sample. The problem with parametric ComBat is that it is based on a Normal-Normal hierarchical model, and even the non-parametric version assumes normal data (but non-parametric priors). For small sample sizes, say 50 miRNAs and say 5-10 samples, the Normal assumptions might be a bad idea. However with your large numbers I think ComBat should work fine. Let me know how it goes!

Thanks!

Evan



On Nov 12, 2012, at 4:01 PM, Simona Rossi wrote:

> Hello Evan,
> 
>   thank you very much for the prompt answer!
> 
> Well, I might give it a try then: I have 755 miRNAs (after filtering ~600 of them will survive) and 400 samples, what do you think?
> 
> Best, Simona
> 
> On Mon, Nov 12, 2012 at 9:55 PM, W. Evan Johnson <wej@bu.edu> wrote:
> Hey Simona, 
> 
> Thanks for your email. This is a difficult question. If the number of samples and number of miRNAs in the data are large, then I think it would be safe to apply ComBat to the data. The non-parametrix prior option might be best. For small sample or miRNA sizes, I don't think there is a good tool out there at the moment.
> 
> I'd be interested to see how it works on your data. Thanks! 
> 
> Evan
> 
> 
> 
> On Nov 12, 2012, at 3:45 PM, Simona Rossi wrote:
> 
>> Hello,
>> 
>>     I'm Simona and I'm a Bioinformatician.
>> 
>> I'm studying some miRNASeq data that are affected by a
>> strong batch effect, in your opinion, ComBat might be
>> applied to miRNASeq data?
>> 
>> Thank you very much in advance,
>> 
>> Best Regards,
>> 
>> Simona Rossi
>> 
>> -- 
>> --
>> Dr. Simona Rossi
>> Bioinformatician
>> 
>> SIB | Swiss Institute of Bioinformatics
>> 
>> Quartier Sorge
>> Bâtiment Génopode
>> CH-1015 Lausanne
>> Switzerland
>> 
>> simona.rossi@isb-sib.ch
>> www.isb-sib.ch
>> 
> 
> 
> 
> 
> -- 
> --
> Dr. Simona Rossi
> Bioinformatician
> 
> SIB | Swiss Institute of Bioinformatics
> 
> Quartier Sorge
> Bâtiment Génopode
> CH-1015 Lausanne
> Switzerland
> 
> t       +41 21 692 40 83
> f       +41 21 692 40 55
> 
> simona.rossi@isb-sib.ch
> www.isb-sib.ch
> 


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