How to apply ComBat on test set for which you do not have the label?

Question

[chengzhao41]

I want to know how I can apply ComBat on the training and test set, if I do not have the labels for test set.

[Devon Ryan]

What exactly do you mean by training and test sets in this context? You run Combat on a group of samples with a known batch-effect and experimental design.

[chengzhao41]

ComBat requires as input a model matrix for outcome of interest, but I only have it for the trianing set and not the test set.

[Devon Ryan]

There are no training and test sets with Combat. There is only a single set of data.

[chengzhao41]

Yes I want to use ComBat to combine training and test set, which are 2 batches, into 1 single set of data. But I do not have the outcome of interest for the test set (2nd batch).