how to remove batch effect in CellID

[anyang-kevin]

Hi,
I'm processing some data with batch effect. Those batch effect may harm to MCA and make many cell can't annotation.
I want to know how to remove it.
I have 2 guesses, but I don't know which is the right way.

1. use integration method. I try to use harmony before annotation. But harmony and MCA don't seem to be compatible.Please tell me if I can use integration algorithms and how to use them.
2. Run Cellid on each sample separately. Is this a viable approach, or make some mistakes?

Hope for your reply.

[Cortalak]

Hi,

You can chose both approach however one is simpler.

1. You can use integration methods but it needs to have some kind of corrected matrix output which for the case of harmony isn't really the case so this one is a bit difficult as most batch effect correction methods are only correcting the dimension reduction.
2. The one I would choose is the second one which is performing the annotation on each sample separately which can be tedious but at least won't rely on any external tools.