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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