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how to deal with batcheffect if the analysis needs to be done on raw count data? #15

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ygz605500160 opened this issue Oct 8, 2022 · 1 comment
Open

how to deal with batcheffect if the analysis needs to be done on raw count data? #15

ygz605500160 opened this issue Oct 8, 2022 · 1 comment

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@ygz605500160
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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 ygz605500160 reopened this Oct 17, 2022
@ygz605500160
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i just read the VISION paper and noticed the authors recommended normalizing batch effect before performing the analysis.

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