[BioC] DEXSeq- ExonCountSet

Steve Lianoglou lianoglou.steve at gene.com
Thu Apr 10 20:17:01 CEST 2014


On Thu, Apr 10, 2014 at 11:01 AM, Anitha Sundararajan <asundara at ncgr.org> wrote:
> Thanks Jim!
> I should have noticed that.  I had to import paths for R, gcc and other libs
> and re-load the package.  That solved it.
> But I am running into another problem at the same step.
> When I run
> ecs <- read.HTSeqCounts(sampleTable$countFile, sampleTable,
> "Arabidopsis_thaliana.modified.flattened.gff")
> I now get,
> Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) :
>   'file' must be a character string or connection
> Can you please help me out with this error.

The elements in sampleTable$countFile aren't proper paths to the files
where the count data are stored.


R> file.exists(sampleTable$countFile)

This is likely because you have a relative path encoded in
`sampleTable$countFile` and it is incorrect given the directory R is
running in (which is `getwd()`)

Perhaps you can fix it by putting absolute file paths in
`sampleTable$countFile` or starting R from a more appropriate


Steve Lianoglou
Computational Biologist

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