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Published 20 hours ago • verified publisher icon immunogenomics

ups and downs in the standard deviation

Open showteeth opened this issue 3 years ago • 1 comments

Hi, Thanks for providing Harmony for the integration of single-cell data.
When using ElbowPlot to select dimensions for downstream analysis, I noticed that there are ups and downs in the standard deviation (in the following figure), is this normal? To my knowledge, the standard deviation of principal components in PCA is in decreasing order. Why does this happen?

plot_zoom_png

showteeth avatar Oct 19 '22 09:10 showteeth

same question. Is it ok to reorder the harmony pcs and select the ones that explain the most variance?

iichelhadi avatar Nov 27 '23 05:11 iichelhadi