dupRadar density scatter plot interpretation problem
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Greta • 0
Last seen 16 months ago


I have obtained dupRadar density scatter plots and I have problems on interpretation. My plot looks just like dupRadar vignettes example of good density scatter plot (https://bioconductor.riken.jp/packages/3.6/bioc/vignettes/dupRadar/inst/doc/dupRadar.html) except that the 0.5 RPKM threshold starts a bit below 100 reads/kbp and not right above 10 reads/kbp. What is the reason that the 0.5 RPKM threshold is much higher than on example plot?

Int is 0.11 and Sl 2.62 in my plot (sorry I do not know how to post the image here). Could this be because of technical duplication problem even though the slope looks just fine?

I do not have sessioninfo() because I didn't do this plot by myself but obtained it from nf-core/RNA-seq pipeline.

Thank you for your help in advance!

EDIT: Interestingly, MultiQC summary output of dupRadar show the generalized linear model slopes in one plot and there the 0.5 RPKM (green marker) is marked between 0.1-1 reads/kbp. I would have expected it to show the same theshold level as dupRadar output of single sample. Is it possible that there has been a bug when these images were generated?

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