I used the standard protocol of Cold Spring Harb, and get some .genes.results after most procedures. when I want to import RSEM data, I found that the Rstudio software warned all(file.exists(files)) are true, so how can I solve the problem.

dir <- "/Users/Documents/eQTL_analysis traning"

library(tximport)

library(DESeq2)

samples <- read.table (file.path (dir, "samples.txt"), header=T)

files <- file.path (dir, samples$Sample, paste0(samples$Sample, ".genes.results"))

names(files) <- samples$Sample

txi <- tximport (files, type = "rsem", txIn = FALSE, txOut = FALSE)

Check files to see what files are listed and then figure out which (or all) are not on your machine at the location you specified.

file.exists(files)

R will not guess the right location for you. You have to specify the correct location, relative to your current working directory or using absolute paths.