Hi, The plotMD get as title the whole file path. How would it be possible to have e.g. only the file name rather than the whole path as plot title?

library(edgeR)
# where are we?
basedir <- "~/projects/mel/Sp/"
setwd(basedir)

tayets <- read.delim("phenoSp.txt", stringsAsFactors=FALSE)
tayets

## ----group---------------------------------------------------------------
group <- paste(tayets$CellType, tayets$Status, sep=".")
group <- factor(group)
table(group)


cntdir <- paste(basedir, "Htseq_read_counts", sep="/")
pat <- "sorted.out"
files <- list.files(path = cntdir,
                    pattern = pat,
                    all.files = TRUE,
                    recursive = FALSE,
                    ignore.case = FALSE,
                    full.names = TRUE,
                    include.dirs = FALSE)

files
y <- readDGE(files, header=FALSE, group = group)
y

# Filtering to remove low counts
keep <- rowSums(cpm(y)>1) >= 2
table(keep)

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

# Normalization for composition bias
y <- calcNormFactors(y)
y$samples

#Exploring differences between libraries
## ----mdsplot, fig.cap="The MDS plot of the data set. Samples are separated by the cell type in the first dimension, and by the mouse status in the second dimension."----
pch <- c(0,1,2,15,16,17)
colors <- rep(c("darkgreen", "red", "blue"), 2)
plotMDS(y, col=colors[group], pch=pch[group])
legend("topleft", legend=levels(group), pch=pch, col=colors, ncol=2)

## ----mdplot1, fig.cap="MD plot of log2-expression in sample 1 versus the average log2-expression across all other samples. Each point represents a gene, and the red line indicates a log-ratio of zero. The majority of points cluster around the red line."----
plotMD(y, column=1)
abline(h=0, col="red", lty=2, lwd=2)

Thank you in advance.

By default, the column names of y are just the entries from your files vector. To control the plot title, you either reset the column names of y by

colnames(y) <- whatever you want

or use the main argument of plotMD() to set your own title:

plotMD(y, column=1, main="MD plot of my first sample")