How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
Hey, I have tried harmony or CCA for batch effect correction for my single-cell RNA-seq data to compare the differeces between tumor and normal tissues, but I found that when I tried to integrate all the samples by harmony or CCA, the results showed an over-correction between tumor and normal tissues, e.g. exhausted T cells, which were only present in tumors, could be found on normal tissues after batch effect correction. How can I solve this problem? Can I solved this problem by modifying some of the parameters in RUNHarmony or Findintegrationanchors function? or any function else?
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