lcpm <- cpm(y2, log=TRUE)
boxplot(lcpm, las=2, col=group$Sample, main="")
title(main="A. Example: Unnormalised data",ylab="Log-cpm")
The boxplot I got was
Why don't I get normal boxplot after using above command ?
Maybe you have too many outliers (the bars seem indeed to be squeezed at the bottom of the plot). What happens if you use:
boxplot(lcpm, las = 2, col = group$Sample, main = "", outline = FALSE)
Try a violin or joy plot rather than a box plot.
@kevin , I tried with your code but did not work, unfortunately.
Me? ...or do you mean Devon (sounds similar), or my colleague in Ireland, SelenoCysteine?
I'd like to hear the accent where Kevin/Devon sound like selenocysteine :)
Urrgh... maybe in Irish
Ancient gaelic indeed. Anyway, what do you mean it doesn't work? Which error message do you get?
Try mean-centering your data with the log scale transformation.
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