boxplot in edgeR

Question

[Björn]

par(mfrow=c(1,2))      
lcpm <- cpm(y2, log=TRUE)             
boxplot(lcpm, las=2, col=group$Sample, main="")       
title(main="A. Example: Unnormalised data",ylab="Log-cpm")

The boxplot I got was

https://ibb.co/bZ8RQn

Why don't I get normal boxplot after using above command ?

[Selenocysteine]

Maybe you have too many outliers (the bars seem indeed to be squeezed at the bottom of the plot). What happens if you use:

boxplot(lcpm, las = 2, col = group$Sample, main = "", outline = FALSE)

?

[Devon Ryan]

Try a violin or joy plot rather than a box plot.

[Björn]

@kevin , I tried with your code but did not work, unfortunately.

[Kevin Blighe]

Me? ...or do you mean Devon (sounds similar), or my colleague in Ireland, SelenoCysteine?

[Devon Ryan]

I'd like to hear the accent where Kevin/Devon sound like selenocysteine :)

[Kevin Blighe]

Urrgh... maybe in Irish

[Selenocysteine]

Ancient gaelic indeed. Anyway, what do you mean it doesn't work? Which error message do you get?

Answer 1

[theobroma22]

Try mean-centering your data with the log scale transformation.