... When you merge the colData and your data.frame you end up changing the rownames of the resulting DataFrame, which is where the colnames come from. You could just do
cn <- colnames(aems450k1.MvaluesQCIMPplaqueSE)
colData(aems450k1.MvaluesQCIMPplaqueSE) <- merge(colData(aems450k1.MvaluesQCIMP ...
... Any time you see an error like
there is no package called 'GenomeInfoDbData'
That is intended to be informative, and means that you are missing a package called GenomeInfoDbData. The cure for that error is to install
and then go back and try to install minfi again ...
If you use makeTxDbFromBiomart, you get a TxDb based on EBI/EMBL mappings, which is not the same as NCBI. UCSC is technically not the same either, but it is very close, and one could argue a bit cleaner.
... You can just add your own, using the points function.
volcanoplot(fit2,coef="Diff.1", names=fit$genes$NAME, main="mDC vs iDC")
lp <- -log10(fit2$p.value[,"Diff.1"])
ord <- order(lp, decreasing = TRUE)[1:10]
points(fit2$coef[ord,"Diff.1"], lp[ord], pch = 16, cex = 0.45, col = 2)