plotSmear() function in edgeR

[Martin Umhang]

Hi all,

I have used edgeR to analyse my Illumina RNAseq data. It generally works fine and I get biologically meaningfull DGE results.

I appreciate that plotSmear() is able to visualize the tags with no counts in one of the libraries. I am unsure however, as to what value is used to plot these tags on the logFC-Axis.

I have not been able to find this in the edgeR-manual or Mark Robinson's /Davis McCarthy's paper. Any ideas on this would be appreciated!

Best,

martin

[A Oshlack]

The value on the Y-axis for these points is log2(counts) if the first library is non-zero or -log2(counts) if the second library is non-zero.