Error in plotting Enhanced Volcano plot
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0
Entering edit mode
15 months ago
Sib ▴ 20

I performed a differential expression analysis of microarray data. Now, I have a top table (tT) of results. The tT has logFC, adj.P.Val, GENE-SYMBOL columns. I want to plot a volcano plot by EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling so I enter these codes:

library(EnhancedVolcano)
EnhancedVolcano(tT, lab = tT$GENE_SYMBOL, x = 'logFC', y = 'adj-P-Val', xlim = c(-6, 6),title = 'Volcano plot', pCutoff = 0.01, FCcutoff = 1.5,pointSize = 2.0,labSize = 2.0)

and I get this error:

Error in EnhancedVolcano(tT, lab = tT$GENE_SYMBOL, x = "logFC", y = "adj-P-Val",  : 
  adj-P-Val is not numeric!

But actually the class of adj-P-Val is numeric

class(tT$adj.P.Val)
[1] "numeric"

How can I fix it?

differential expression analysis enhanced volcano • 864 views
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Entering edit mode
15 months ago
dsull ★ 1.8k

Hello, the column name in your dataframe is adj.P.Val, not adj-P-Val. Therefore, when you call EnhancedVolcano, you should use:

EnhancedVolcano(tT, lab = tT$GENE_SYMBOL, x = 'logFC', y = 'adj.P.Val', xlim = c(-6, 6),title = 'Volcano plot', pCutoff = 0.01, FCcutoff = 1.5,pointSize = 2.0,labSize = 2.0)

If you want to preserve the name adj-P-Val with the hyphens instead of periods, when you first create your data frame, you should use the parameter: check.names=FALSE. This will permit the code you wrote in your original post to work.

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Thanks for answering.

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Please don't delete a question after you received help. The content might be useful for someone else. We don't answer questions just for you but for the entire community.

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I already have up-voted to the answer and ticked accept and after that, I deleted the post because I thought that it was not useful for the entire community.

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