[BioC] DESeq- figures on variance estimation

Melissa.Martin at lshtm.ac.uk Melissa.Martin at lshtm.ac.uk
Tue Mar 27 13:53:12 CEST 2012

Hi Wolfgang,

Thank you for you for your help with the volcano plot, I was able to get it to work.

I am trying to make Figures on variance estimation as shown in Supplementary II (4.3). 
What function should I use for 'varianceFitDiagnostics' ?

Many Thanks,


Dear Melissa

does the code work for you if you reproduce it exactly from the example? 
Once that is established, you could start making changes and then see 
when what breaks.

Also, why do you want to set log="x"? The data that you are supplying 
for the x-axis, log2FoldChange, are already on the log-scale, so that 
argument does not seem necessary (in fact: wrong).

Also, if the complexity of lattice of plots is overwhelming, you can 
always use the basic R plots:

   plot( log2FoldChange, -log10( pval ) )

Best wishes

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