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satijalab / sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
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Is it OK to use SCTransform on SoupX modified data? #139

Closed kaizen89 closed 1 year ago

kaizen89 commented 1 year ago

Hi, I am wandering if it is OK to use SCTransform on SoupX modified data knowing that these data contain double instead of integer values? Thanks

saketkc commented 1 year ago

You may want to run SoupX using roundToInt=TRUE to round off the estimates to nearest integer and then run SCTransform.

haoyanioz commented 1 year ago

Dear developer @saketkc , I wanna ask if it is OK to use SCTransform to normalize directly on SoupX-corrected decimal counts (roundToInt=FALSE). Does it have any bad effects? Because I did that (roundToInt=FALSE), and there were no errors reported.

You may want to run SoupX using roundToInt=TRUE to round off the estimates to nearest integer and then run SCTransform.