Question: Error in DESeq analysis directory argument - No such file or directory
gravatar for AW
14 months ago by
AW0 wrote:


I'm using DESeq2 for RNA-Seq data analysis. Everything looks great but I get an error about my directory at the final step even though I'm in the correct working directory

sampleCondition <- read.table(file=sampleFiles, header = TRUE, sep = "", row.names = 1)

sampleTable <- data.frame(sampleName = sampleFiles, fileName = sampleFiles, condition = samplecondition)

> getwd()
[1] "C:/Users/xyz/Downloads"

directory <- "/Users/xyz/Downloads/FeatureCounts.txt"
 ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,directory = directory, design = ~condition)

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/Users/xyz/Downloads/FeatureCounts.txt/0': No such file or directory

please help! I'm pretty sure the directory exists and that I am currently working in that directory (see getwd). Everything else in the analysis looks good

hts rna-seq deseq • 568 views
ADD COMMENTlink written 14 months ago by AW0

If sampleFiles are in the directory: "C:/Users/xyz/Downloads", try directory <- "C:\\Users\\xyz\\Downloads"?

ADD REPLYlink written 14 months ago by SMK1.9k
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