tximport error importing expected counts file from RSEM
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Muyu • 0
@Muyu-24524
Last seen 12 months ago

Hi,

I have this gene_expected_count.txt generated from RSEM and I am trying to use tximport to upload files into R, then use DESeq2 to do downstream analysis. The file has gene_id and then a coulmn for each sample (total sample = 6)

library(tximportData)
dir <- setwd(".")
list.files(dir)
samples <- read.table(file.path(dir, "gene_expected_count.txt"), header = TRUE)
samples
files <- file.path(dir, "gene_expected_count.txt", samples, paste0(samples, "gene_expected_count.txt"))
names(files) <- paste0("sample", 2:7)
#txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)

#Error in tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE) : 
  all(file.exists(files)) is not TRUE

This is the error that I keep getting and I have tried everything from files.exist(dir) and I get back a TRUE

Can someone tell me where I am going wrong? I am totally new to R and analyzing RNA-seq data

RSEM tximport • 240 views
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Entering edit mode
@mikelove
Last seen 22 hours ago
United States

That error says that the files don't exist at the locations you've specified. You can just look at files[1] to debug.

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