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Error converted from warning #159

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Echoloria opened this issue Jun 3, 2024 · 1 comment
Open

Error converted from warning #159

Echoloria opened this issue Jun 3, 2024 · 1 comment

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@Echoloria
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Hi,
thanks for developing such a powerful tool.

When I run these code:
sc = setContaminationFraction(sc, 0.2)
out = adjustCounts(sc)

I got an error:
Error in sparseMatrix(i = out@i[w] + 1, j = out@j[w] + 1, x = out@x[w], :
(converted from warning) 'giveCsparse' is deprecated; setting repr="T" for you

The packages I used are as below: Seurat(v4.4.0), Soupx(v1.6.2)
I searched this error in the "issues" part, but I didn't find the same error that anyone who have met.
So, is there anything wrong with the version of packages I'm using?

@Dongjie-orange
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Dongjie-orange commented Aug 7, 2024

the same question I met, this question may raised because SoupX generated an non-integer matrix where the original counts have been corrected for background expression, see https://rawcdn.githack.com/constantAmateur/SoupX/204b602418df12e9fdb4b68775a8b486c6504fe4/inst/doc/pbmcTutorial.html

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