Error in plotMA while using limma package
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Entering edit mode
14 months ago
mrinsmrids • 0

I have been experiencing an error while using the limma package in R to plot the top gene but unfortunately, I have been getting an error stating I do not have two columns The piece of code looks like this:

 limma::plotMA(c(resSig$log2FoldChange,resSig$pvalue),alpha = 0.05, colNonSig = "grey",ylim = c(-5,5))

The error I am getting is :

Error in plotMA.default(c(resSig$log2FoldChange, resSig$pvalue), alpha = 0.05, : Need at least two columns.

My resSig contains the following :

enter image description here

limma • 341 views
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1
Entering edit mode
14 months ago

without data and with data images, it is not easy to troubleshoot the query. I would suggest to try:

$ limma::plotMA(cbind(resSig$log2FoldChange,resSig$pvalue),alpha = 0.05, colNonSig = "grey",ylim = c(-5,5))

or

 $ limma::plotMA(matrix(c(resSig$log2FoldChange,resSig$pvalue), ncol=2),alpha = 0.05, colNonSig = "grey",ylim = c(-5,5))

If resSig is one of the following objects, you can use maplot function directly on them: an RGList, MAList, EList, ExpressionSet or MArrayLM object. (copy/pasted from the manual)

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