object 'missing.populations' not found

[debsXXCIII]

Hi @ebecht

I am trying to use MCP Counter and I get the following error:

Error in MCPcounter.estimate(data, featuresType = "ENTREZID", genes = genes) :
object 'missing.populations' not found

Here are my commands:

data <- read.csv("C:/Users//Documents/MCPCounter/MCP_data.csv",header = TRUE,sep = ",",row.names = 1, check.names = FALSE)

genes=read.table("C:/Users/dguest/Documents/MCPCounter/genes.txt",header = TRUE,sep = "\t",row.names = 1, check.names = FALSE)

result<-MCPcounter.estimate(data, featuresType="ENTREZID", genes=genes)

Please could you let me know how I can debug this?

Many thanks

Deborah

[ebecht]

Hi,

Please try:
result<-MCPcounter.estimate(data, featuresType="ENTREZ_ID", genes=genes)

Thank you

[debsXXCIII]

Hi @ebecht

Unfortunately this still generates the same error, I made sure that the headings had the same spellings.

Thanks

[ebecht]

Hi @debsXXCIII

What do you mean by "the headings had the same spellings" ? The call should still be using featuresType="ENTREZ_ID" even if the corresponding column in the genes data.frame is named "ENTREZID"

[ebecht]

Closing this, feel free to re-open if that issue wasn't solved