Question: ComBat correction with one batch containing only one sample - keep or remove?
gravatar for Sebastian Hesse
20 months ago by
Germany / Munich / Dr. von Hauner Children's Hospital
Sebastian Hesse110 wrote:

I am using sea analysis and combat to correct a proteome dataset. During the correction process ComBat tells me that one batch contains only one sample. Apparently this leads to a modification of the method used:

Note: one batch has only one sample, setting mean.only=TRUE

My question is of this is ok or if I should rather remove this one sample from my analysis so ComBat can run normally?

Thanks a lot! Sebastian

R combat sva proteome • 636 views
ADD COMMENTlink modified 17 months ago by Biostar ♦♦ 20 • written 20 months ago by Sebastian Hesse110

I use ComBat for batch effect removal, too. From my understanding, it removes the batch effect through adjusting the data mean and variance from different bathes. If one of your batches contains only one sample, there is no way that ComBat can remove the variance (since there is no variance), and it has to set mean.only=T. If that one-sample batch is important to your analysis, in my opinion, it is totally ok to keep it and use the mean.only=T ComBat. If you have a lot of samples and you do not care about throwing away that one sample, then removing it you should be able to use mean.only=F setting. I would suggest doing PCA before and after you apply ComBat and see how ComBat has changed your data. That might give you some idea of whether including or excluding that one sample.

ADD REPLYlink modified 20 months ago • written 20 months ago by miaowzai230

Thanks, I removed it form the analysis at the end.

ADD REPLYlink written 17 months ago by Sebastian Hesse110
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