[BioC] edgeR maPlot - plotting group means?

[Mark Robinson]

Hi Iddo.

Have a look at the plotSmear() function (see page 46 of the user's guide, for example).

Cheers,
Mark

On 2010-09-12, at 9:40 PM, Iddo Ben-Dov wrote:

> Dear all,
> 
> I am a novice edgeR user.
> 
> The edgeR manual describes the steps to produce an maPlot from 2 groups of samples, page 5/58 in:
> http://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeR.pdf
> 
> par(mfrow = c(1, 2))
> maPlot(D[, 1], D[, 2], normalize = TRUE, pch = 19, cex = 0.2, ylim = c(-8, 8))
> grid(col = "blue")
> abline(h = log2(f[2]), col = "red", lwd = 4)
> maPlot(d$counts[, 1]/d$samples$lib.size[1], d$counts[, 2]/d$samples$lib.size[2], normalize = FALSE, pch = 19, cex = 0.2, ylim = c(-8, 8))
> grid(col = "blue")
> 
> 
> I suspect that the commands plot samples 1 and 2 and NOT groups 1 and 2.
> Am I correct? 
> What can I do to actually look at group comparisons?
> 
> Thanks,
> Iddo
> 	[[alternative HTML version deleted]]
> 
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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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