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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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Setting contamination rate manually does not emprove the correction #69

Closed akramdi closed 3 years ago

akramdi commented 3 years ago

Hello,

Following the recommendations on when a data still looks contaminated after correction, I tried increasing the contamination rate from the estimated one using HB genes (%3) to 10%, then 20% using:

conta=0.1 #or 0.2 sc=setContaminationFraction(sc,conta) out = adjustCounts(sc, roundToInt=TRUE)

This does not change the contamination: it looks unchanged and I still see background expression of a gene in clusters where it should not be expressed (this was also confirmed by plotMarkerMap plot)

Are these the right command ? We just need to set the contamination then adjust the count, right?

Thanks for the help. Best,

constantAmateur commented 3 years ago

plotMarkerMap does not plot the corrected counts, you need some downstream tool (like Seurat) to do that. The code you have described will change the contamination rate and result in a different output matrix. If you want to confirm this, store both versions and then check if out1 == out2.