Hello everyone,

I'm new to bioinformatic in general and R too, and i am taking the workshop of DGE analysis overview: https://hbctraining.github.io/DGEworkshopsalmon/lessons/01DGEsetupandoverview.html.

Unfortunately, i can not follow the step with the provided code: Salmon (quant.sf) to tximport

## List all directories containing data           samples <- list.files(path = "./data", full.names = T, pattern="salmon$")
## Obtain a vector of all filenames including the path               files <- file.path(samples, "quant.sf")
## Since all quant files have the same name it is useful to have names for each element        names(files) <- str_replace(samples, "./data/", "") %>%    str_replace(".salmon", "")

It showed files character(0) and samples character(empty) in value. But there are quant.sf files in each sample file(.salmon)

And i have written the whole path for this codes, it is yet not working well. Wish for someone to help me figure out the problem. Thanks a lot.

So you have:

samples <- list.files(path = "./data", full.names = T, pattern="salmon$")

Then

files <- file.path(samples, "quant.sf")

If files is an empty vector, then samples is an empty vector, so then you need to figure out why there are no directories starting with salmon... in the data directory relative to your current working directory.