Hello,

I'm working with transcript IDs as the species I'm working with is a non-model, so now that I managed to produce Volcanoplots from the contrasts:

Example:

cont.matrix1 <- makeContrasts(ConeVsRoot=Cone-Root, levels=design)
fit.cont <- contrasts.fit(fit, cont.matrix1)
fit.cont <- eBayes(cont.matrix1)
summa.fit <- decideTests(cont.matrix1)
summary(cont.matrix1)
volcanoplot(fit.cont,coef=1, highlight=50, names=seqdata$Transcript, main="ConeVsRoot", pch=10, cex=0.25)

My question is for one, how I can have the top 50 as a data frame so do GO and KEGG (since I need the IDs to retrieve the sequences from the original assembly)? Also, I shortened the IDs and dropped the non-unique characters but still cannot have the whole name and it's not unique yet. For example, this is an ID, "DN523_c0" on the plot as it only shows 7 characters, but the complete ID is "DN523_c0_g1_i1" which is unique while the former is not. How I can expand the number of characters for IDs?

Appreciate your comments and opinions.

how I can have the top 50 as a data frame

topTable()

How I can expand the number of characters for IDs

volcanplot() will only plot the first 8 characters of each gene name (because it seems hardly useful to crowd a plot with long names). If you want to plot longer names then you need to add them to the plot yourself using R's text() function.