boxplot in edgeR
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3.2 years ago
Björn ▴ 60
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 boxplot lcpm • 1.7k views
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1
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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)

?

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

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

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

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

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Urrgh... maybe in Irish

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

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3.2 years ago
theobroma22 ★ 1.1k

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

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