@Kevin, That was indeed the issue.
Thanks
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peter.berry5 •
Using the Enhanced Volcano plot results in a "subscript out of bounds" error
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.
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peter.berry5 •
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It seems that the issue is lowercase 'l' versus uppercase 'L' on Log2FC
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Kevin Blighe
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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.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
was wrong. it should be
However, I now get a different error which is
running
str(volcano_attached)to check if the column Log2FC is numeric givesSo I'm still stuck. If you can spot any other error that would be great.