Volcano plot non-numeric argument error
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elena.capel ▴ 10
@elenacapel-12192
Last seen 7.8 years ago

Hi there,

I'm trying to draw a volcano plot using some scripts that I found in a very handy manual:

http://www.nathalievilla.org/doc/pdf/tutorial-rnaseq.pdf

The problem is that I get an error that I don't manage to overcome:

> str(resEdgeR)
Classes ‘tbl_df’, ‘tbl’ and 'data.frame':    1405 obs. of  6 variables:
 $       : chr  "NMA0001" "NMA0002" "NMA0003" "NMA0004" ...
 $ logFC : num  -0.27 -6.43 0.56 -4.5 -6.54 ...
 $ logCPM: num  7.71 8.58 9.37 3.69 5.74 ...
 $ LR    : num  0.0521 17.0523 0.2248 8.2597 12.7363 ...
 $ PValue: num  0.8194151 0.0000364 0.6354217 0.0040534 0.0003586 ...
 $ FDR   : num  0.916079 0.000896 0.825109 0.023191 0.004031 ...
> tab = data.frame(logFC = resEdgeR$table[, 1], negLogPval = -log10(resEdgeR$table[, 4]))
Error in log10(resEdgeR$table[, 4]) : 
non-numeric argument for a mathematical fonction

The error tells me that my argument is non-numeric, however when I get the structure of my data frame it states that it is numeric though. Any suggestion how to solve this problem?

Many thanks in advance!

volcano plot edgr • 2.0k views
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It looks like the 1st column of your data corresponds to  $   : chr  "NMA0001" "NMA0002" "NMA0003" "NMA0004" so you're numeric columns are off by one, is it any better if you try  tab = data.frame(logFC = resEdgeR$table[, 2], negLogPval = -log10(resEdgeR$table[, 5]))

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That's not the problem since when I type head(tab) I can visualize the columns I selected:

> tab = data.frame(logFC = resEdgeR$table[, 1], negLogPval = -log10(resEdgeR$table[, 4]))
Error in log10(resEdgeR$table[, 4]) : 
  argument non numérique pour une fonction mathématique
> head(tab)
       logFC           Pval
1 -0.2698253 0.819415130920
2 -6.4312079 0.000036364860
3  0.5601794 0.635421715093
4 -4.5000469 0.004053371323
5 -6.5425931 0.000358625306
6 -7.8980613 0.000006034407

But I still have the problem of calculating the log10 for one of the variables. 

> class(tab[,"Pval"])
[1] "numeric"
> log10("Pval")
Error in log10("Pval") : 
  argument non numérique pour une fonction mathématique
 

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Did you really mean log10("Pval"), rather than log10(tab[,"Pval"]) ?

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You're right, my command was bad. Now if I try your command the calculation is made.

The problem is that I can't manage to create a new data frame with one intact variable (logFC) and the new calculate variable (-log10(Pval)):

> tab = data.frame(logFC = resEdgeR$table[, 1], negLogPval = -log10(tab[,"Pval"]))
Error in data.frame(logFC = resEdgeR$table[, 1], negLogPval = -log10(tab[,  : 
  les arguments impliquent des nombres de lignes différents : 0, 1405

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It's probably down to the capitalisation of the table names - (you had a lower-case v in pvalue), and also you were referencing tab in the creation of tab itself: try

tab = data.frame(logFC = resEdgeR$table$logFC, negLogPval = -log10(resEdgeR$table$PValue))


 

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Thanks a lot but I keep having the same error:

> tab = data.frame(logFC = resEdgeR$table$logFC, negLogPval = -log10(resEdgeR$table$PValue))
Error in log10(resEdgeR$table$PValue) : 
  argument non numérique pour une fonction mathématique

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hmm, running out of options without seeing the data; try using 'head', 'summary' and maybe 'plot' on the column resEdgeR$table$PValue to see if there's any clues as to where the non-numeric values are creeping in.

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I'll keep trying tomorrow and let you informed of any hopefully advances!

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Hi Gavin,

Actually I was doing a very basic mistake not calling the variables properly.

I wrote resEdgeR$table[, 1] or resEdgeR$table$logFC

when I should have actually written: resEdgeR[, 1] or resEdgeR$logFC

Thanks anyway for your help!

 

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