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PCA is very slow on large single-cell matrices #17

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lwaldron opened this issue Jun 23, 2022 · 1 comment
Open

PCA is very slow on large single-cell matrices #17

lwaldron opened this issue Jun 23, 2022 · 1 comment
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lwaldron commented Jun 23, 2022 •
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Consider using irlba for very large matrices, or allowing use of pre-computed PCA from other packages as input to 1validate()1.
@shbrief shbrief self-assigned this Jun 24, 2022
@shbrief shbrief added the enhancement New feature or request label Jun 24, 2022
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lwaldron commented Jun 25, 2022 •
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(used to be, "consider using scater::runPCA / scater::calculatePCA", changed after discussion with Vince). irlba has an advantage of only one dependency (Matrix), and allowing computation of only the desired number of PCs. If you go the route of using irlba, I would suggest using it all the time rather than only for larger matrices, for the sake of simplicity and not having to have two different sets of code.

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