Hi Rishi, Sorry no idea. You should follow up with the USeq maintainers. Mike On Jul 26, 2014 8:17 PM, "Rishi Sinha" <rishi.z.sinha@berkeley.edu> wrote: > 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 > > -- > [[alternative HTML version deleted]]