ups and downs in the standard deviation

immunogenomics / harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

https://portals.broadinstitute.org/harmony/

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ups and downs in the standard deviation #175

Open showteeth opened 2 years ago

showteeth commented 2 years ago

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

iichelhadi commented 11 months ago

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