[BioC] DEXSeq- ExonCountSet
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$countFile, sampleTable,
> I now get,
> Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) :
> 'file' must be a character string or connection
> Can you please help me out with this error.
The elements in sampleTable$countFile aren't proper paths to the files
where the count data are stored.
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
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