Display error (error bars) for fold-change estimate from replicates in edgeR
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tstueve • 0
@tstueve-8014
Last seen 8.8 years ago
United States

Greetings,

 

  I have used edgeR to calculate fold-changes in gene expression between treated and untreated cells, each group consisting of three replicates. The boss would very much like me to display some estimate of error in fold-change for genes of our immediate interest. Is there a way to do this in edgeR? I have not found any leads in newer vignettes.

Thanks very much,

   Ryan   

 

edger rnaseq • 2.3k views
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Aaron Lun ★ 28k
@alun
Last seen 2 hours ago
The city by the bay

Check out A: Confidence intervals on edgeR logFC. In short, there is no easy way to get a reliable error estimate for the log-fold changes in edgeR. If you really need confidence intervals, then try using voom instead. Just set confint=TRUE when running topTable in limma.

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