[BioC] baySeq plotPosteriors or plotMA question

Smith, Hilary A hilary.smith at gatech.edu
Wed Nov 2 18:17:22 CET 2011

I'm a graduate student and just starting to analyze my first set of RNA-Seq data (so learning R/Bioconductor). In using the baySeq program, I am slightly confused about how to color-code the significant values in the plotPosteriors (and plotMA) functions. 

The vignette includes the example below to color-code differentially expressed genes as red.
> plotPosteriors(CDPost.NBML, group = 2, samplesA = 1:5, samplesB = 6:10, col = c(rep("red", 100), rep("black", 900)))

However, I believe the use of 100 for the red (and 900 for the black / not differentially expressed) is specific to their simulated data set. Is this correct, and if so, how can I make the function more general to plot the differentially expressed genes for any data set?

Thank you,

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