Hi Elena, On Fri, Feb 17, 2012 at 10:11 AM, Elena Sorokin <sorokin at="" wisc.edu=""> wrote: > Dear Alejandro, > > I can't seem to find the development version that you were talking about. I > am running the version available for BioC 2.9: > http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq. html > > ...Could you tell me where to download v 1.1.6 of your software? The *-devel biocundoctor packages can be found here: http://www.bioconductor.org/packages/devel/bioc/ Officially speaking, in order to run these, you should also be using the "-devel" version of R, ie. snapshots of R from current SVN. Calls to biocLite will then fetch from the bioc devel repo. Unofficially, you can hack around this by installing this by hand, but you'd be asking for trouble. Depending on the type of system (mac/linux/win), installing a working version of R-devel can be super easy (or less so). For instance, on a mac, you can get an installer for R-devel here: http://r.research.att.com/ Other people can suggest how to do so for other systems ... HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Dear Elena, You can always use the svn to get the latests versions: http://www.bioconductor.org/developers/source-control/ Bests, Alejandro > Dear Alejandro, > > I can't seem to find the development version that you were talking > about. I am running the version available for BioC 2.9: > http://watson.nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq. html > > ...Could you tell me where to download v 1.1.6 of your software? > > Thanks, > Elena > > On 2/17/2012 6:11 AM, Alejandro Reyes wrote: >> Dear Elena, >> >> I am glad you like the package! >> We recently fixed this bug, it should be fine if you use the most >> recent development >> version of DEXSeq (1.1.6) >> >> This should be solved by then, if not, could you send me your ecs >> object to give it a >> closer look? >> >> Thanks! >> >> Alejandro >> >> >> Greetings all, >> >> I ran into another problem with the DEXseq program, and I was hoping >> that somebody could help me once more. I successfully ran through a >> full analysis of one time point of my dataset, and was hoping ideally to >> extend the analysis to my full time course, using the GLM test. However, >> I ran into this error when running fitDispersionFunction: >> >> > ecs<- fitDispersionFunction(ecs) >> Warning messages: >> 1: In glmgam.fit(mm, disps[good], start = coefs) : >> Too much damping - convergence tolerance not achievable >> 2: In glmgam.fit(mm, disps[good], start = coefs) : >> Too much damping - convergence tolerance not achievable >> >> I couldn't find the answer in the list archive. Do the DEXseq authors or >> anyone else know what this error means? >> >> I'd be truly grateful for any advice about this - I really like the >> DEXseq package, and I'm hoping to use/reference it in my manuscript if I >> can get it to work! My full script is below. >> >> Sincerely, >> Elena >> ------------------------------------- >> > library(DEXSeq) >> > annotationfile = file.path("../DEXSeq_annotations.gff") >> > annotationfile >> [1] "../DEXSeq_annotations.gff" >> > samples<- read.table("PLdesign.txt",header=T,row.names=1) >> > samples >> treatment time >> PL_D1hr_1 vehicle one >> PL_D1hr_2 vehicle one >> PL_U1hr_1 drug one >> PL_U1hr_2 drug one >> PL_D2hr_1 vehicle two >> PL_D2hr_2 vehicle two >> PL_U2hr_1 drug two >> PL_U2hr_2 drug two >> PL_D4hr_1 vehicle four >> PL_D4hr_2 vehicle four >> PL_U4hr_1 drug four >> PL_U4hr_2 drug four >> PL_D6hr_1 vehicle six >> PL_D6hr_2 vehicle six >> PL_U6hr_1 drug six >> PL_U6hr_2 drug six >> > fullFilenames<- list.files(full.names=TRUE,pattern="exon.txt") >> > fullFilenames >> [1] "./PL_1hrD1_exon.txt" "./PL_1hrD2_exon.txt" "./PL_1hrU1_exon.txt" >> [4] "./PL_1hrU2_exon.txt" "./PL_2hrD1_exon.txt" "./PL_2hrD2_exon.txt" >> [7] "./PL_2hrU1_exon.txt" "./PL_2hrU2_exon.txt" "./PL_4hrD1_exon.txt" >> [10] "./PL_4hrD2_exon.txt" "./PL_4hrU1_exon.txt" "./PL_4hrU2_exon.txt" >> [13] "./PL_6hrD1_exon.txt" "./PL_6hrD2_exon.txt" "./PL_6hrU1_exon.txt" >> [16] "./PL_6hrU2_exon.txt" >> > ecs<- read.HTSeqCounts(countfiles = fullFilenames,design = >> samples,flattenedfile = annotationfile) >> # Check out ecs object >> > head(counts(ecs)) >> ./PL_1hrD1_exon.txt ./PL_1hrD2_exon.txt ./PL_1hrU1_exon.txt >> 2L52.1:001 12 16 7 >> 2L52.1:002 32 22 19 >> 2L52.1:003 18 16 14 >> 2L52.1:004 19 16 20 >> 2L52.1:005 28 22 9 >> 2L52.1:006 19 15 22 >> ./PL_1hrU2_exon.txt ./PL_2hrD1_exon.txt ./PL_2hrD2_exon.txt >> 2L52.1:001 4 7 4 >> 2L52.1:002 19 23 16 >> 2L52.1:003 20 15 17 >> 2L52.1:004 11 8 17 >> 2L52.1:005 17 23 27 >> 2L52.1:006 20 19 23 >> ./PL_2hrU1_exon.txt ./PL_2hrU2_exon.txt ./PL_4hrD1_exon.txt >> 2L52.1:001 2 4 0 >> 2L52.1:002 18 13 13 >> 2L52.1:003 15 5 15 >> 2L52.1:004 12 4 8 >> 2L52.1:005 18 14 13 >> 2L52.1:006 15 10 13 >> ./PL_4hrD2_exon.txt ./PL_4hrU1_exon.txt ./PL_4hrU2_exon.txt >> 2L52.1:001 2 1 1 >> 2L52.1:002 9 6 8 >> 2L52.1:003 5 3 17 >> 2L52.1:004 2 3 7 >> 2L52.1:005 17 4 5 >> 2L52.1:006 16 4 6 >> ./PL_6hrD1_exon.txt ./PL_6hrD2_exon.txt ./PL_6hrU1_exon.txt >> 2L52.1:001 4 2 0 >> 2L52.1:002 20 13 4 >> 2L52.1:003 8 7 7 >> 2L52.1:004 7 4 6 >> 2L52.1:005 14 16 9 >> 2L52.1:006 12 13 6 >> ./PL_6hrU2_exon.txt >> 2L52.1:001 2 >> 2L52.1:002 12 >> 2L52.1:003 8 >> 2L52.1:004 4 >> 2L52.1:005 6 >> 2L52.1:006 4 >> > design(ecs) >> treatment time >> ./PL_1hrD1_exon.txt vehicle one >> ./PL_1hrD2_exon.txt vehicle one >> ./PL_1hrU1_exon.txt drug one >> ./PL_1hrU2_exon.txt drug one >> ./PL_2hrD1_exon.txt vehicle two >> ./PL_2hrD2_exon.txt vehicle two >> ./PL_2hrU1_exon.txt drug two >> ./PL_2hrU2_exon.txt drug two >> ./PL_4hrD1_exon.txt vehicle four >> ./PL_4hrD2_exon.txt vehicle four >> ./PL_4hrU1_exon.txt drug four >> ./PL_4hrU2_exon.txt drug four >> ./PL_6hrD1_exon.txt vehicle six >> ./PL_6hrD2_exon.txt vehicle six >> ./PL_6hrU1_exon.txt drug six >> ./PL_6hrU2_exon.txt drug six >> > head(fData(ecs)) >> geneID exonID testable dispBeforeSharing dispFitted >> dispersion >> 2L52.1:001 2L52.1 E001 NA NA >> NA NA >> 2L52.1:002 2L52.1 E002 NA NA >> NA NA >> 2L52.1:003 2L52.1 E003 NA NA >> NA NA >> 2L52.1:004 2L52.1 E004 NA NA >> NA NA >> 2L52.1:005 2L52.1 E005 NA NA >> NA NA >> 2L52.1:006 2L52.1 E006 NA NA >> NA NA >> pvalue padjust chr start end strand transcripts >> 2L52.1:001 NA NA chrII 1867 1911 + 2L52.1 >> 2L52.1:002 NA NA chrII 2506 2694 + 2L52.1 >> 2L52.1:003 NA NA chrII 2738 2888 + 2L52.1 >> 2L52.1:004 NA NA chrII 2931 3036 + 2L52.1 >> 2L52.1:005 NA NA chrII 3406 3552 + 2L52.1 >> 2L52.1:006 NA NA chrII 3802 3984 + 2L52.1 >> # All in all, Exon Count Set looks good >> > ecs<- estimateSizeFactors(ecs) >> > sizeFactors(ecs) >> ./PL_1hrD1_exon.txt ./PL_1hrD2_exon.txt ./PL_1hrU1_exon.txt >> ./PL_1hrU2_exon.txt >> 1.7543472 1.6354950 1.6969669 >> 1.5496025 >> ./PL_2hrD1_exon.txt ./PL_2hrD2_exon.txt ./PL_2hrU1_exon.txt >> ./PL_2hrU2_exon.txt >> 1.4932349 1.3392481 1.4051111 >> 1.1780430 >> ./PL_4hrD1_exon.txt ./PL_4hrD2_exon.txt ./PL_4hrU1_exon.txt >> ./PL_4hrU2_exon.txt >> 0.9026051 0.5879963 0.5206059 >> 0.5726255 >> ./PL_6hrD1_exon.txt ./PL_6hrD2_exon.txt ./PL_6hrU1_exon.txt >> ./PL_6hrU2_exon.txt >> 0.7345296 0.7536120 0.7763199 >> 0.7529934 >> > formuladispersion<- count ~ sample + ( exon + treatment ) * time >> > ecs<- estimateDispersions( ecs, formula = formuladispersion, >> nCores=11) >> Estimating Cox-Reid exon dispersion estimates using 11 cores. (Progress >> report: one dot per 100 genes) >> ................................................................... ...................................................................... .................> >> >> >> > /usr/local/lib64/R/library >> > ecs<- fitDispersionFunction(ecs) >> Warning messages: >> 1: In glmgam.fit(mm, disps[good], start = coefs) : >> Too much damping - convergence tolerance not achievable >> 2: In glmgam.fit(mm, disps[good], start = coefs) : >> Too much damping - convergence tolerance not achievable >> >> > sessionInfo() >> R version 2.14.0 (2011-10-31) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] multicore_0.1-7 DEXSeq_1.0.2 Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] hwriter_1.3 plyr_1.7.1 statmod_1.4.14 stringr_0.6 >> tools_2.14.0 >> > >> >

Dear Elena, To access the latest version of any Bioconductor package (available only from the development branch), you need to run the development version of R. To get access to that package you need to be running R-2.15 and install BioC 2.10. R-2.14.1 and BioC 2.9, which I presume you are running, are the current stable version for which you can only get DEXSeq version 1.0.2. Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On 17 Feb 2012, at 16:11, Elena Sorokin wrote: > Dear Alejandro, > > I can't seem to find the development version that you were talking about. I am running the version available for BioC 2.9: http://watson. nci.nih.gov/bioc_mirror/packages/2.9/bioc/html/DEXSeq.html > > ...Could you tell me where to download v 1.1.6 of your software? > > Thanks, > Elena > > On 2/17/2012 6:11 AM, Alejandro Reyes wrote: >> Dear Elena, >> >> I am glad you like the package! >> We recently fixed this bug, it should be fine if you use the most recent development >> version of DEXSeq (1.1.6) >> >> This should be solved by then, if not, could you send me your ecs object to give it a >> closer look? >> >> Thanks! >> >> Alejandro >> >> >> Greetings all, >> >> I ran into another problem with the DEXseq program, and I was hoping >> that somebody could help me once more. I successfully ran through a >> full analysis of one time point of my dataset, and was hoping ideally to >> extend the analysis to my full time course, using the GLM test. However, >> I ran into this error when running fitDispersionFunction: >> >> > ecs<- fitDispersionFunction(ecs) >> Warning messages: >> 1: In glmgam.fit(mm, disps[good], start = coefs) : >> Too much damping - convergence tolerance not achievable >> 2: In glmgam.fit(mm, disps[good], start = coefs) : >> Too much damping - convergence tolerance not achievable >> >> I couldn't find the answer in the list archive. Do the DEXseq authors or >> anyone else know what this error means? >> >> I'd be truly grateful for any advice about this - I really like the >> DEXseq package, and I'm hoping to use/reference it in my manuscript if I >> can get it to work! My full script is below. >> >> Sincerely, >> Elena >> ------------------------------------- >> > library(DEXSeq) >> > annotationfile = file.path("../DEXSeq_annotations.gff") >> > annotationfile >> [1] "../DEXSeq_annotations.gff" >> > samples<- read.table("PLdesign.txt",header=T,row.names=1) >> > samples >> treatment time >> PL_D1hr_1 vehicle one >> PL_D1hr_2 vehicle one >> PL_U1hr_1 drug one >> PL_U1hr_2 drug one >> PL_D2hr_1 vehicle two >> PL_D2hr_2 vehicle two >> PL_U2hr_1 drug two >> PL_U2hr_2 drug two >> PL_D4hr_1 vehicle four >> PL_D4hr_2 vehicle four >> PL_U4hr_1 drug four >> PL_U4hr_2 drug four >> PL_D6hr_1 vehicle six >> PL_D6hr_2 vehicle six >> PL_U6hr_1 drug six >> PL_U6hr_2 drug six >> > fullFilenames<- list.files(full.names=TRUE,pattern="exon.txt") >> > fullFilenames >> [1] "./PL_1hrD1_exon.txt" "./PL_1hrD2_exon.txt" "./PL_1hrU1_exon.txt" >> [4] "./PL_1hrU2_exon.txt" "./PL_2hrD1_exon.txt" "./PL_2hrD2_exon.txt" >> [7] "./PL_2hrU1_exon.txt" "./PL_2hrU2_exon.txt" "./PL_4hrD1_exon.txt" >> [10] "./PL_4hrD2_exon.txt" "./PL_4hrU1_exon.txt" "./PL_4hrU2_exon.txt" >> [13] "./PL_6hrD1_exon.txt" "./PL_6hrD2_exon.txt" "./PL_6hrU1_exon.txt" >> [16] "./PL_6hrU2_exon.txt" >> > ecs<- read.HTSeqCounts(countfiles = fullFilenames,design = >> samples,flattenedfile = annotationfile) >> # Check out ecs object >> > head(counts(ecs)) >> ./PL_1hrD1_exon.txt ./PL_1hrD2_exon.txt ./PL_1hrU1_exon.txt >> 2L52.1:001 12 16 7 >> 2L52.1:002 32 22 19 >> 2L52.1:003 18 16 14 >> 2L52.1:004 19 16 20 >> 2L52.1:005 28 22 9 >> 2L52.1:006 19 15 22 >> ./PL_1hrU2_exon.txt ./PL_2hrD1_exon.txt ./PL_2hrD2_exon.txt >> 2L52.1:001 4 7 4 >> 2L52.1:002 19 23 16 >> 2L52.1:003 20 15 17 >> 2L52.1:004 11 8 17 >> 2L52.1:005 17 23 27 >> 2L52.1:006 20 19 23 >> ./PL_2hrU1_exon.txt ./PL_2hrU2_exon.txt ./PL_4hrD1_exon.txt >> 2L52.1:001 2 4 0 >> 2L52.1:002 18 13 13 >> 2L52.1:003 15 5 15 >> 2L52.1:004 12 4 8 >> 2L52.1:005 18 14 13 >> 2L52.1:006 15 10 13 >> ./PL_4hrD2_exon.txt ./PL_4hrU1_exon.txt ./PL_4hrU2_exon.txt >> 2L52.1:001 2 1 1 >> 2L52.1:002 9 6 8 >> 2L52.1:003 5 3 17 >> 2L52.1:004 2 3 7 >> 2L52.1:005 17 4 5 >> 2L52.1:006 16 4 6 >> ./PL_6hrD1_exon.txt ./PL_6hrD2_exon.txt ./PL_6hrU1_exon.txt >> 2L52.1:001 4 2 0 >> 2L52.1:002 20 13 4 >> 2L52.1:003 8 7 7 >> 2L52.1:004 7 4 6 >> 2L52.1:005 14 16 9 >> 2L52.1:006 12 13 6 >> ./PL_6hrU2_exon.txt >> 2L52.1:001 2 >> 2L52.1:002 12 >> 2L52.1:003 8 >> 2L52.1:004 4 >> 2L52.1:005 6 >> 2L52.1:006 4 >> > design(ecs) >> treatment time >> ./PL_1hrD1_exon.txt vehicle one >> ./PL_1hrD2_exon.txt vehicle one >> ./PL_1hrU1_exon.txt drug one >> ./PL_1hrU2_exon.txt drug one >> ./PL_2hrD1_exon.txt vehicle two >> ./PL_2hrD2_exon.txt vehicle two >> ./PL_2hrU1_exon.txt drug two >> ./PL_2hrU2_exon.txt drug two >> ./PL_4hrD1_exon.txt vehicle four >> ./PL_4hrD2_exon.txt vehicle four >> ./PL_4hrU1_exon.txt drug four >> ./PL_4hrU2_exon.txt drug four >> ./PL_6hrD1_exon.txt vehicle six >> ./PL_6hrD2_exon.txt vehicle six >> ./PL_6hrU1_exon.txt drug six >> ./PL_6hrU2_exon.txt drug six >> > head(fData(ecs)) >> geneID exonID testable dispBeforeSharing dispFitted dispersion >> 2L52.1:001 2L52.1 E001 NA NA NA NA >> 2L52.1:002 2L52.1 E002 NA NA NA NA >> 2L52.1:003 2L52.1 E003 NA NA NA NA >> 2L52.1:004 2L52.1 E004 NA NA NA NA >> 2L52.1:005 2L52.1 E005 NA NA NA NA >> 2L52.1:006 2L52.1 E006 NA NA NA NA >> pvalue padjust chr start end strand transcripts >> 2L52.1:001 NA NA chrII 1867 1911 + 2L52.1 >> 2L52.1:002 NA NA chrII 2506 2694 + 2L52.1 >> 2L52.1:003 NA NA chrII 2738 2888 + 2L52.1 >> 2L52.1:004 NA NA chrII 2931 3036 + 2L52.1 >> 2L52.1:005 NA NA chrII 3406 3552 + 2L52.1 >> 2L52.1:006 NA NA chrII 3802 3984 + 2L52.1 >> # All in all, Exon Count Set looks good >> > ecs<- estimateSizeFactors(ecs) >> > sizeFactors(ecs) >> ./PL_1hrD1_exon.txt ./PL_1hrD2_exon.txt ./PL_1hrU1_exon.txt >> ./PL_1hrU2_exon.txt >> 1.7543472 1.6354950 1.6969669 >> 1.5496025 >> ./PL_2hrD1_exon.txt ./PL_2hrD2_exon.txt ./PL_2hrU1_exon.txt >> ./PL_2hrU2_exon.txt >> 1.4932349 1.3392481 1.4051111 >> 1.1780430 >> ./PL_4hrD1_exon.txt ./PL_4hrD2_exon.txt ./PL_4hrU1_exon.txt >> ./PL_4hrU2_exon.txt >> 0.9026051 0.5879963 0.5206059 >> 0.5726255 >> ./PL_6hrD1_exon.txt ./PL_6hrD2_exon.txt ./PL_6hrU1_exon.txt >> ./PL_6hrU2_exon.txt >> 0.7345296 0.7536120 0.7763199 >> 0.7529934 >> > formuladispersion<- count ~ sample + ( exon + treatment ) * time >> > ecs<- estimateDispersions( ecs, formula = formuladispersion, nCores=11) >> Estimating Cox-Reid exon dispersion estimates using 11 cores. (Progress >> report: one dot per 100 genes) >> ................................................................... ...................................................................... .................> >> >> > /usr/local/lib64/R/library >> > ecs<- fitDispersionFunction(ecs) >> Warning messages: >> 1: In glmgam.fit(mm, disps[good], start = coefs) : >> Too much damping - convergence tolerance not achievable >> 2: In glmgam.fit(mm, disps[good], start = coefs) : >> Too much damping - convergence tolerance not achievable >> >> > sessionInfo() >> R version 2.14.0 (2011-10-31) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] multicore_0.1-7 DEXSeq_1.0.2 Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] hwriter_1.3 plyr_1.7.1 statmod_1.4.14 stringr_0.6 >> tools_2.14.0 >> > >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor