Harmony integration PC variance explained

Question

[e.iich]

Hi guys,

I ran harmony on my seurat obj and then elbow plot to select the number of PCs for downstream analysis. I found that a number of the earlier PCs explain less variance than the subsequent PCs

I am not sure how this is possible. Does this indicate that there is something wrong with batch effect correction? Also, I was wondering if it is acceptable to reorder the PCs based on explained variance and to use those for downstream analyses?

Regards

[CTLong]

After batch correction, the gene expression values will change based on the modelling or anchoring algorithm you chose to use. If the top PCs explained less variance, this simply means that the genes were given a lower weight after integration, hence a lower sum of explained variance by the PC.

To check if your batch correction has succeeded, one way is to take the top PCs and perform a dimension reduction analysis. See if the samples are positionally arranged based on biological relevance rather than technical batch.