I'm posting this error here to have a clearer idea of what's going on.
I'm running tximport using my own dataset and following and modifying the instructions on the vignette. But I have found an issue and I can't get around it.
I have specified my working directory under the variable dir as follows:
dir <- '/Users/ctl/data/samples/experiment/salmon'
and I have created my files as follows:
files <- file.path(dir, samples$run, "quant.genes.sf")
which gives me an output like this:
Now, if I add the sample name as follows:
names(files) <- paste0(samples$run)
I get this:
And this result agrees with what I have in that directory and inside each sample folder. However, when I check if all files are listed, I get this error:
In my previous (misplaced) post on GitHub issues, I was told that I am not providing the right directory for the files, but it seem I am providing it correctly. Any hints to how can I solve this problem?
Thanks in advance!