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wu-yc / scMetabolism

Quantifying metabolism activity at the single-cell resolution
BSD 3-Clause "New" or "Revised" License
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how to deal with batcheffect if the analysis needs to be done on raw count data? #15

Open ygz605500160 opened 1 year ago

ygz605500160 commented 1 year ago

hi ~ i am new to this package. i tried to run the analysis on an integrated dataset and the results appears to be significantly affected by batcheffect. i checked the source code and noticed that the package uses raw count data from the "RNA" slot. how should i deal with batcheffect if the analysis needs to be done on raw count data? thanks.

ygz605500160 commented 1 year ago

i just read the VISION paper and noticed the authors recommended normalizing batch effect before performing the analysis.