Hi,

Ok, I did that, and now I have some error basically before DESeq2 can
basically even run, it's erroring about not being able to find a results
file? Is there a subdirectory/file I should be creating for it to log
things?

Excerpt of output is below:

Running DESeq2 analysis...
java.io.IOException:

R results file doesn't exist. Check temp files in sav
e directory for error.

        at edu.utah.seq.analysis.DefinedRegionDiffere
ntialSeq.runDESeq2(DefinedRegionDifferentialSeq.java:
1033)
        at edu.utah.seq.analysis.DefinedRegionDiffere
ntialSeq.run(DefinedRegionDifferentialSeq.java:148)
        at edu.utah.seq.analysis.DefinedRegionDiffere
ntialSeq.<init>(DefinedRegionDifferentialSeq.java:99)
        at edu.utah.seq.analysis.DefinedRegionDiffere
ntialSeq.main(DefinedRegionDifferentialSeq.java:1698)
Error: failed to execute DESeq2.l-144


The command I'm using is :
java -jar ~/bin/USeq_8.8.1/Apps/DefinedRegionDifferentialSeq -s
~/DiffSeq/ResultsTimeSet1/ -c ~/DiffSeq/TimeSet1/ -g hg19 -u
~/hg19ucsc.gz

if that helps at all.

I've been trying to mess around with my directories to see if I could
create something that it would accept, but not getting anywhere, and I
didn't think I could access the code for DESeq2 in its package to see what
its looking for, so I'm really stuck.

Thanks for the prompt help earlier; any further help troubleshooting this
would be very much appreciated, as well as any tips for how to solve things
like this in the future.

Thanks again!
Rishi


On Sat, Jul 26, 2014 at 3:39 AM, Michael Love <michaelisaiahlove@gmail.com>
wrote:

> Hi Rishi,
>
> This is a version difference between what you have on your machine and
> what the script uses. Use the help() or ? function in.R to access the
> correct documentation for your version.
>
> You can either update R to get the release version of Bioconductor, or
> create an alias:
>
> rlog = rlogTransformation
> On Jul 26, 2014 12:12 AM, "Rishi [guest]" <guest@bioconductor.org> wrote:
>
>> Hello!
>>
>> I'm trying to use USeq's Defined Region Differential Seq (DRDS) app,
>> which uses DESeq2.
>>
>> I installed the package directly from Bioconductor, and but when running
>> the script, I get an error that the function rlog() couldn't be found. I
>> looked up rlog in DESeq and only found rlogTransformation().
>>
>> I believe that's an error in DESeq2, but I'm kind of new to all this so
>> I'm not sure. Does anyone have any suggestions on what steps to take to fix
>> this?
>>
>> Thank you very much in advance :)
>>
>> Sincerely,
>> Rishi
>>
>>  -- output of sessionInfo():
>>
>> > #get and save rlog transformed
>> > rld = rlog(cds)
>> Error: could not find function "rlog"
>> Execution halted
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
>


-- 

--
Rishi Sinha
University of California, Berkeley
B.A. Computer Science | 2016
B.A. Molecular and Cellular Biology | 2016

--

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