I want to make a geneList for clusterProfiler analysis but I get "error in do.call( cbind lapply(x is.na )) variable names are limited to 10000 bytes"
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Emilia ▴ 30
@emiliabaffo
Last seen 4 months ago

Hello! I have a data frame with differential expression analysis which looks like this

head(DEedgeR)
ENTREZID logFC
<chr>    <dbl>
1 10       -2.43
2 18       -1.05
3 20        1.01
4 21        2.29
5 24        2.27
6 25        1.12


I tried creating a geneList arguement like it's described here https://github.com/YuLab-SMU/DOSE/wiki/how-to-prepare-your-own-geneList

geneList = DEedgeR[,2]
names(geneList)= as.character(DEedgeR[,1]) #up until here it was okay
#but when I ran this last part
geneList = sort(geneList, decreasing = TRUE)
#I got this
Error in do.call("cbind", lapply(x, "is.na")) :
variable names are limited to 10000 bytes


I don't know what's wrong since I followed the same steps which were described on the github resource I cited above. My dataset has over 6400 genes but I guess that's not such an oddly elevated amount in this type of analysis. Also, I tried using the geneList object I created above as an argument for the gseGO function just to see what happened and I got the same error message about the 10000 bytes. Sorry if it's too silly but I really hope someone can help me!

clusterProfiler • 474 views
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What if you explicitly set logFC as numeric? Thus: geneList = as.numeric( DEedgeR[,2] )

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I tried doing it like that but I got "Error: 'list' object cannot be coerced to type 'double'"

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Then it seems to me that your object DEedgeR is not a data frame... (but maybe a tibble?) What does: class(DEedgeR) return?

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Thanks! it was in fact a tibble, I first ran the as.data.frame(DEedgeR) command then proceeded to do it as I had already tried above and it worked! Thank you so much, I was so worried about the issue being something about the syntax or the function itself that I hadn't even thought it could be simply an object class problem.