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ups and downs in the standard deviation #175

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showteeth opened this issue Oct 19, 2022 · 1 comment
Open

ups and downs in the standard deviation #175

showteeth opened this issue Oct 19, 2022 · 1 comment

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

@iichelhadi iichelhadi mentioned this issue Nov 29, 2023
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@showteeth @iichelhadi