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
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