Question: boxplot in edgeR
0
gravatar for Björn
19 months ago by
Björn40
Björn40 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 • 935 views
ADD COMMENTlink modified 19 months ago by theobroma221.1k • written 19 months ago by Björn40
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 19 months ago • written 19 months ago by Selenocysteine550

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

ADD REPLYlink written 19 months ago by Devon Ryan91k

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

ADD REPLYlink written 19 months ago by Björn40

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

ADD REPLYlink modified 19 months ago • written 19 months ago by Kevin Blighe48k
1

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

ADD REPLYlink written 19 months ago by Devon Ryan91k

Urrgh... maybe in Irish

ADD REPLYlink written 19 months ago by Kevin Blighe48k

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

ADD REPLYlink written 19 months ago by Selenocysteine550
0
gravatar for theobroma22
19 months ago by
theobroma221.1k
theobroma221.1k wrote:

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

ADD COMMENTlink written 19 months ago by theobroma221.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1695 users visited in the last hour