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Question: rlog() not in DESeq2?
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4.2 years ago by
Guest User12k
Guest User12k 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.
ADD COMMENTlink modified 4.2 years ago by Michael Love19k • written 4.2 years ago by Guest User12k

Hi Rishi, 

 

Were you ever able to work out how to get around this issue? I'm having the same error as well...

 

Thanks,
Fran

ADD REPLYlink written 3.6 years ago by franziska.denk0
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gravatar for Michael Love
4.2 years ago by
Michael Love19k
United States
Michael Love19k 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. > [[alternative HTML version deleted]]
ADD COMMENTlink written 4.2 years ago by Michael Love19k
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]]
ADD REPLYlink written 4.2 years ago by Rishi Sinha10
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]]
ADD REPLYlink written 4.2 years ago by Michael Love19k
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