What's wrong with my data or code?

Question

[ys19f]

I have already had a set of RSEM data, and want to calculate the expression difference. My code is shown below, but I don't know what's wrong with it. It always tells me all(file.exists(files)) is not TRUE. How can I fix this problem?

library(tximport)
library(DESeq2)
dir <- c("~/sy/Desktop/Course/2019-2020/Bioinformatics/Assignment2/RSEM")
samples <- c("Ap03","Ap07","CLP2700","CLP2701","KW1750","KW1996","KW2031","KW2035","MM0024")
samples <- sort(samples)
files <- file.path(dir,paste0(samples,".genes.results"))
names(files) <- samples
txi.rsem <- tximport(files,type = "rsem", txIn=FALSE, txOut = FALSE)
head(txi.rsem$counts)
sampleTable <- data.frame(condition = factor(c(rep("A",5),rep("J",5))))
rownames(sampleTable) <- colnames(txi.rsem$counts)
dds <- DESeqDataSetFromTximport(txi.rsem, sampleTable, ~condition)
dds <- DESeq(dds)
res <- results(dds, contrast=c("condition","A","J"))
res <- res[order(res$pvalue),]
summary(res)
write.csv(res, file="results.csv")

[ATpoint]

According to the manual (https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#rsem) the RSEM outputs are gzipped, is this the case here?

files <- file.path(dir, "rsem", samples$run, paste0(samples$run, ".genes.results.gz"))
names(files) <- paste0("sample", 1:6)
txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)

[Kevin Blighe]

Also what are the actual contents of files?

[cpad0112]

what part of the code is throwing error? In each step, try to check the object, start with samples, followed by other objects such as files, sampleTable and further downstream. @ ys19f

[weichengz]

Hi, I got the same problem. Did you manage to fix it?