What's wrong with my data or code?
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")
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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?
Also what are the actual contents of
files?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
Hi, I got the same problem. Did you manage to fix it?