Question: boxplot in edgeR
0
gravatar for Björn
2.8 years ago by
Björn50
Björn50 wrote:
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 ?

edger lcpm boxplot • 1.5k views
ADD COMMENTlink modified 2.8 years ago by theobroma221.1k • written 2.8 years ago by Björn50
1

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)

?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Selenocysteine600

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

ADD REPLYlink written 2.8 years ago by Devon Ryan97k

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

ADD REPLYlink written 2.8 years ago by Björn50

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

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Kevin Blighe67k
1

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

ADD REPLYlink written 2.8 years ago by Devon Ryan97k

Urrgh... maybe in Irish

ADD REPLYlink written 2.8 years ago by Kevin Blighe67k

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

ADD REPLYlink written 2.8 years ago by Selenocysteine600
0
gravatar for theobroma22
2.8 years ago by
theobroma221.1k
theobroma221.1k wrote:

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

ADD COMMENTlink written 2.8 years ago by theobroma221.1k
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