Question: boxplot in edgeR
0
gravatar for Björn
4 months ago by
Björn20
Björn20 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 • 310 views
ADD COMMENTlink modified 4 months ago by theobroma221.1k • written 4 months ago by Björn20
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 4 months ago • written 4 months ago by Selenocysteine460

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

ADD REPLYlink written 4 months ago by Devon Ryan80k

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

ADD REPLYlink written 4 months ago by Björn20

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

ADD REPLYlink modified 4 months ago • written 4 months ago by Kevin Blighe21k
1

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

ADD REPLYlink written 4 months ago by Devon Ryan80k

Urrgh... maybe in Irish

ADD REPLYlink written 4 months ago by Kevin Blighe21k

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

ADD REPLYlink written 4 months ago by Selenocysteine460
0
gravatar for theobroma22
4 months ago by
theobroma221.1k
theobroma221.1k wrote:

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

ADD COMMENTlink written 4 months ago by theobroma221.1k
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