I have bulk RNASeq data in TPM format. I could see from doing an initial PCA that there were issues with batch effects with this data. So I did ComBat Normalisation which seems to improve this. However, I am really confused about the data I have from running ComBat on my data. The majority of the data is integers and then a handful of the data are floats. I don't understand why this is? I should add that prior to doing ComBat normalisation on this dataset, I did log2 + 1.
Please could someone tell me if: 1) it's ok to carry out combat on data in TPM format 2) is it ok that Log2 transformed the data prior to combat 3) why is the majority of the data integers with some floats? why not all integers or all floats?
Thank you in advance.