[BioC] ComBat: Working with no replicates

[Pekka Kohonen]

Dear Pedro,

If you have just one sample from the lab, how do you differentiate
between the cell line-specific effect and the lab-specific effect? I
don't see how you are trying to do with these 3 samples makes any
sense. If you have the same cell lines measured in a different lab
(which has enough samples to run ComBat) why not just use those then?
Also, I wonder what is the minimum number of samples to estimate a
lab-specific distribution (which is what Combat is doing) for each
gene? Probably 5-10 samples or so?

I think that statistics should not be treated as just a way to hack
your data so that it appears to be OK. This sounds a bit like doing
that. :-)

Best, Pekka

P.S. my name in Finnish means "Pedro"

2013/10/28 Pedro Furió Tarí <pfurio at cipf.es>:
> Dear all,
>
> We have a mix of cell-lines run by 12 different labs (more than 150 samples
> in total) and we have found a strong batch effect by laboratory that we
> would like to correct. From those 12, there are 3 labs that are bringing
> just one cell-line with no replicates at all (1 sample).
>
> If we remove the samples from those 3 labs, we are able to run ComBat, but
> we would like to keep them if possible. Is there any way? If we simulate a
> "false replicate" just by copying the same expression values it works.
> Could it be the way to go? Could these results be trustworthy?
>
> We also would like to use the different cell-line names as the covariates,
> but some of them don't have any replicates, so it doesn't work. Is there
> any way we could also use them as categorical covariates? Right now we are
> not giving any covariates information.
>
> Any help would be much appreciated :)
>
> Thanks in advance,
>
> Pedro
>
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>
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