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immunogenomics / harmony

Fast, sensitive and accurate integration of single-cell data with Harmony
https://portals.broadinstitute.org/harmony/
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Cell Cycle Regression and ScaleData #162

Closed adri-biochem closed 2 years ago

adri-biochem commented 2 years ago

Hello,

I am looking to use harmony integration on my dataset and compare SCTransform vs. LogNormalize for downstream analysis. I have a pretty homogenous group of cells that should not be grouped by cell cycle phase based on other biological factors. For the SCTransform method, I am able to regress this out when I run the SCTransform function and everything runs fine. However, when I use LogNormalize and re-run ScaleData before harmony integration (as suggested in issue #117) I am still unable to regress out cell cycle. I tried moving the ScaleData step to other locations in my code, such as right after the RunHarmony step and after the FindClusters step. However, I still get the same graph. Any suggestions on how to proceed? Thank you!

adri-biochem commented 2 years ago

Forgot to re-run PCA after ScaleData step and that fixed the issue.