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 ______________________________________________________________________ ________________________________________________ Martin Umhang PhD Student D-Biol, ETH Z?rich LFW, E54 Universit?tstr. 2 8092 Z?rich Tel.: 044 6325948 (Lab) 044 6323839 (Office)

Hi Martin. Thanks for pointing this out. We should add this detail to the help doc or manual. Here is the (somewhat formal) definition. Say X_i is your count for (gene k from) one sample and Y_k is the count for the other sample, n_X, n_Y is the library size (or effective library size after calculating normalization factors). Now, say X_k=0 and Y_k>0. logFC = log2( [0/n_X] / [Y_k/n_Y] ) is not going to work, so we simply replace that with log2( [(0+X*)/n_X] / [Y_k/n_Y] ) where X* is the minimum count greater than 0. Often, this will be 1 and so you are effectively treating 0s as 1s for the calculation. Same for both directions. This is of course just a visualization and all of these points are shown in the separated smear part of the plot anyways. Hope that makes sense. Cheers, Mark > 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 > ____________________________________________________________________ __________________________________________________ > Martin Umhang > PhD Student > D-Biol, ETH Z?rich > LFW, E54 > Universit?tstr. 2 > 8092 Z?rich > > Tel.: 044 6325948 (Lab) > 044 6323839 (Office) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}