Hello Davis,

Here is the history of the codes:
d <- DGEList(counts = d, group = group)
d
d <- estimateCommonDisp(d)
d <- estimateTagwiseDisp(d, prior.n = 10, grid.length = 500)
prior.n <- estimateSmoothing(d)
prior.n
de.tgw <- exactTest(d, common.disp = FALSE)
de.tgw
sum(de.tgw$table$p.value < 0.01)
sum(de.tgw$table$p.value > 0.01)
detags.tgw <- rownames(topTags(de.tgw, n = sum(de.tgw$table$p.value <
0.01))$table)
plotSmear(d, de.tags = detags.tgw, main = "FC Plot using tagwise
dispersion")
abline(h = c(-2, 2), col = "dodgerblue", lwd = 2)
plotSmear(d, de.tags = detags.tgw, main = "FC Plot using tagwise
dispersion", cex=0.8, pch=plotsymbols)
plotSmear(d, main = "FC Plot using tagwise dispersion", cex=0.8,
pch=plotsymbols)
de <- as.logical(abs(decideTestsDGE(d)))
Error in decideTestsDGE(d) : Need DGEExact or DGELRT object

I guess this error message is because all my objects are in DGEList.
Any other code that I could use to get the plot in Black and White with
different shapes for non-DE and DE will be highly appreciated.


Thanks,
Sridhara




On Wed, Apr 13, 2011 at 10:48 PM, Davis McCarthy <dmccarthy@wehi.edu.au>wrote:

> Hi Sridhara
>
> Remember that all of the usual R plotting commands can be passed to
> plotSmear in the '...' argument (see ?plotSmear). You can just change the
> pch argument as required (the standard R parameter for plotting symbol).
>
> This code is one way of doing what you want to do (assuming that your DE
> results are in a DGEExact or DGELRT object called "results"):
>
> de <- as.logical(abs(decideTestsDGE(results)))
> plotsymbols <- rep(19, nrow(results))
> plotsymbols[de] <- 4
> plotSmear(results, cex=0.8, main="MA Plot", pch=plotsymbols)
>
> This will give you closed circles for non-DE genes and 'x's for DE genes.
> You can play with the choice of symbols as you please.
>
> Cheers
> Davis
>
>
> On Apr 13, 2011, at 11:54 PM, Sridhara Gupta Kunjeti wrote:
>
> > Hello,
> > I have used edgeR for DGE analysis and also generated plotSmear. I guess
> by
> > dufault the plotSmear shows red dots for differentially expressed genes.
> > But, I want to generate a black and white plot, is there a possbility to
> > gene using different shape of the points, may be 'x' for the
> differentially
> > expressed genes.  If any one know how to change this it will be helpful.
> >
> > Many thanks in advance!
> > Sridhara
> >
> >
> > --
> > Sridhara G Kunjeti
> > PhD Candidate
> > University of Delaware
> > Department of Plant and Soil Science
> > email- sridhara@udel.edu
> > Ph: 832-566-0011
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> ------------------------------------------------------------------------
> Davis J McCarthy
> Research Technician
> Bioinformatics Division
> Walter and Eliza Hall Institute of Medical Research
> 1G Royal Parade, Parkville, Vic 3052, Australia
> dmccarthy@wehi.edu.au
> http://www.wehi.edu.au
>
>
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:22}}

