Hi,

I am analyzing RNAseq data using the EdgeR package and have made the MDS plot using the following code.

y<-DGEList(counts=data, group=Source)

keep<- rowSums(cpm(y)>1) >= 1

y<- y[keep, , keep.lib.sizes=FALSE]

y<-calcNormFactors(y)

plotMDS(y, method="bcv",dim= c(1,2), top=1000)

I am wondering if it is possible to obtain the gene names of the top 1000 genes with the greatest biological coefficient of variation.

Many thanks! 

The BCV is just the square root of the tagwise dispersion, so just take the top 1000 genes with the largest tagwise dispersions:

order(y$tagwise.dispersion, decreasing=TRUE)[1:1000]

... after you've run estimateDisp.