Error on make_se

[RTCarmo]

Hello there,

First of all, thanks for the amazing tool!

I'm trying to load some LFQ 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:

 Error: specified 'columns' should be numeric
 Run make_se_parse() with the appropriate columns as argument

I checked the class of each parameter needed for make_se, and they are in the correct classes!

Here is the proteinGroup file and the ExperimentalDesign files.

This is my code:

library("DEP")
library("dplyr")

wd <- "/home/rtorreglosa/Documents/LFQ_analysis/"
setwd(wd)

data_c <- read.table(file = "LFQ_DEP_analysis_adjusted.txt", header=T, sep="\t", stringsAsFactors = FALSE)

data_c_filt <- filter(data_c, Potential.contaminant != "+")

data_c_filt$Gene.names %>% duplicated() %>% any()

data_c %>% group_by(Gene.names) %>% summarize(frequency = n()) %>% 
arrange(desc(frequency)) %>% filter(frequency > 1)

data_c_unique <- make_unique(data_c_filt, "Gene.names", "Protein.IDs", delim = ";")

data_c_filt$name %>% duplicated() %>% any()

data_c_filt$Razor...unique.peptides

LFQ_columns_c <- grep("LFQ.", colnames(data_c_unique))

experimental_design_c <- read.table(file = "LFQ_Exp_Design.txt", header=T, sep="\t", stringsAsFactors = FALSE)

data_c_se <- make_se(data_c_unique, LFQ_columns_c, experimental_design_c)

Any ideas on how to solve this issue are welcome!

Thanks!

Ramon

[RTCarmo]

After some debugging, I discovered the problem was in my input: My decimal separator was a comma! Changing this automatically made the function work!