satijalab/sctransform

Is it OK to use SCTransform on SoupX modified data?

kaizen89 opened this issue · 2 comments

kaizen89 commented

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

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

haoyanioz commented

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.

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