How to visualize Combat-seq corrected counts

Question

[as823jk]

After using Combat-Seq to remove batch effect, I want to visually confirm removal. I tried doing this the way I visually inspected the batch effect in the first place: PCA on VST-transformed counts. But VST-transform cannot be used on negative values (which Combat-Seq has introduced). How can I confirm that the batch effect has been removed then?

I tried PCA on the batch-corrected counts without any further transformations, but there are no clear patterns.

[cfos4698]

Are you sure you didn't use ComBat instead of Combat_seq?

Answer 1

[ATpoint]

ComBat-seq does not produce negative counts but preserves the integer nature. Thats the whole point of the method. Lets see your code and debug the underlying problem.

[as823jk]

Sorry, I accidentally used ComBat! ComBat-seq did not produce negative counts. Thanks for all the help!