Using the Enhanced Volcano plot results in a "subscript out of bounds" error

Question

[peter.berry5]

Hi

I previously posted a question about the Enhanced Volcano package and now have a different issue with a separate dataset. I'm getting a "subscript out of bounds" error. If I understand correctly this results from an index overflow error for a matrix but I have no idea how to fix this.

My code is

attached_rd <- read.csv("C:/PETER PROJECT/3d. Mass Spec Processing/Results of R Analysis/DE Gene Lists/Effect of Serum/WCL Analysis/0% Attached v 5% Attached/DE Cutoff equal 1.2/DE 1-2 Attached Cells DE Gene IDs WCL Apr19 Serum Removal.csv")
 attached_CHO <- distinct(attached_rd, HGNC_Symbol, .keep_all= TRUE)

 volcano_attached <- data.frame(attached_CHO$HGNC_Symbol, attached_CHO$v5.max_fold_change, attached_CHO$v5.Anova..p)
 names(volcano_attached)[1] <- "HGNC_Symbol"
 names(volcano_attached)[2] <- "Log2FC"
 names(volcano_attached)[3] <- "pvalue"
 volcano_attached <- as.numeric(volcano_attached$Log2FC)
str(volcano_attached)

'data.frame':   1757 obs. of  3 variables:
 $ HGNC_Symbol: chr  "ENO1 " "ANXA1 " "TALDO1 " "LTA4H " ...
 $ Log2FC     : num  2.89 4.84 3.1 2.89 3.46 ...
 $ pvalue     : num  4.30e-08 6.39e-08 6.86e-08 8.78e-08 8.84e-08 ...

   EnhancedVolcano(volcano_attached,
     lab = 'volcano_attached$HGNC_Symbol',
     x = 'log2FC',
     y = 'pvalue',
     xlim = c(-10, 10))

if anybody has any suggestions that would be really appreciated.

[ATpoint]

This is not reproducible, if you post this over at Bioc (or stay here since it is most likely not a technical issue that requires the developers expertise) then please add details. Show what is in volcano_attached. Your file path is full of whitespaces, this is something you should avoid by the way.

[peter.berry5]

Updating the post here as per @ATpoint's reply.

The comment about whitespace made me realise that the HGNC_Symbol column had white spaces and while cleaning that up I realised the line

volcano_attached <- as.numeric(volcano_attached$Log2FC)

was wrong. it should be

volcano_attached$Log2FC <- as.numeric(volcano_attached$Log2FC)

However, I now get a different error which is

Error in EnhancedVolcano(volcano_attached, lab = "volcano_attached$HGNC_Symbol",  : 
  log2FC is not numeric!

running str(volcano_attached) to check if the column Log2FC is numeric gives

data.frame':    1757 obs. of  3 variables:
 $ HGNC_Symbol: chr  "ENO1" "ANXA1" "TALDO1" "LTA4H" ...
 $ Log2FC     : num  2.89 4.84 3.1 2.89 3.46 ...
 $ pvalue     : num  4.30e-08 6.39e-08 6.86e-08 8.78e-08 8.84e-08 ...

So I'm still stuck. If you can spot any other error that would be great.

Answer 1

[Kevin Blighe]

It seems that the issue is lowercase 'l' versus uppercase 'L' on Log2FC

[peter.berry5]

@Kevin, That was indeed the issue.

Thanks

[ATpoint]

Please accept the answer if it solved the issue by clicking the checkmark symbol on the left of his answer.