search

arnesmits / DEP

DEP package
26 stars 12 forks source link

Error when making SE #4

Closed SophieS9 closed 5 years ago

SophieS9 commented 5 years ago

Hi Arne,

Not sure if this is an issue for here or for the the bioconductor forum, so let me know if I should re-post there. I'm trying to load some MaxQuant data into DEP following the instructions in the vignette. All going ok until I try to make the summarized experiment when I get the following error:

data_se<- make_se(data_unique, LFQ_columns, experimental_design)
Error: words is not a character vector

I've checked my input files and I can't see any formatting differences between them and the test data, apart from the fact that I'm using the full proteinGroups file.

Here is the input proteinGroups file, the experimental design, and a markdown with my code.

Any ideas as to what's happening are welcome!

Thanks!

Sophie

arnesmits commented 5 years ago

Dear Sophie,

Sorry for the delay in response. The problem is that the string-columns in your data frames are parsed into factors. This is easily circumvented.

data<-read.table("../AP17112_PBMC/Maxwell/Maxwell_proteinGroups_v2.txt", header=TRUE, sep="\t", stringsAsFactors = FALSE) experimental_design<-read.table("../AP17112_PBMC/experimental_design.txt", header=TRUE, sep="\t", stringsAsFactors = FALSE)

After using this, all should work.

Best, Arne