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Steffen, > Sweave("assessNorm.Rnw") > Sweave("assessNorm.Rnw") Writing to file assessNorm.tex Processing code chunks ... 1 : echo term hide (label=load) 2 : term verbatim (label=errorReporting) 3 : echo term verbatim (label=showDavidTilingData) 4 : echo term verbatim (label=probeAnno) 5 : echo term verbatim (label=whPM) 6 : echo term verbatim (label=table) 7 : echo term verbatim (label=selectArrays) 8 : echo term verbatim (label=normalizeByReference) Error: chunk 8 (label=normalizeByReference) Error in vsn(xn, lts.quantile = 0.95, subsample = 2e+05, verbose = verbose) : The likelihood optimization did not converge. A likely reason is that the normalization parameters are not uniquely identifiable from the provided data. Possibly, the columns of the data matrix are exactly co-linear or affine dependent - please verify the data to make sure there were no mix-ups. Enter a frame number, or 0 to exit 1: Sweave("assessNorm.Rnw") 2: driver$runcode(drobj, chunk, chunkopts) 3: RweaveTryStop(err, options) ----- Original Message ----- From: "Steffen Durinck" <durincks@mail.nih.gov> To: "Lana Schaffer" <schaffer at="" scripps.edu=""> Cc: <bioconductor at="" stat.math.ethz.ch=""> Sent: Wednesday, January 03, 2007 10:55 AM Subject: Re: [BioC] .Rnw file > Hi Lana, > > Try: > > Sweave("assessNorm.Rnw") > > best, > Steffen > > Lana Schaffer wrote: >> Hi, >> I am a little confused how to use the .Rnw file to make a vignette. >> Instructions say "source file inst/scripts/assessNorm.Rnw" >> but when I use the command : source("assessNorm.Rnw") >> I get an error: >> Error in parse(file, n = -1, NULL, "?") : syntax error at >> 1: %\VignetteIndexEntry{tilingArray - assess normalization} >> >> probably because it is not an R file. >> Would you straighten me out a bit? >> >> Lana Schaffer >> Biostatistics/Informatics >> The Scripps Research Institute >> DNA Array Core Facility >> La Jolla, CA 92037 >> (858) 784-2263 >> (858) 784-2994 >> schaffer at scripps.edu >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >

Hi Lana, Rnw files, also called Sweave documents, consist of chunks of LaTeX markup and chunks of R code. Sweave documents can be processed using R's Sweave() function to generate a latex file where the R code chunks have been computed. The resulting tex file can then be transformed into a human readable form, such as PDF. So a common workflow is: Sweave("something.Rnw") # quit R pdflatex something.tex # open something.pdf Another useful thing to do with Rnw files is to extract _only_ the R code. This can be achieved using Rtangle(). The result is an R file containing only the code chunks. "Lana Schaffer" <schaffer at="" scripps.edu=""> writes: > Steffen, >> Sweave("assessNorm.Rnw") >> Sweave("assessNorm.Rnw") > Writing to file assessNorm.tex > Processing code chunks ... > 1 : echo term hide (label=load) > 2 : term verbatim (label=errorReporting) > 3 : echo term verbatim (label=showDavidTilingData) > 4 : echo term verbatim (label=probeAnno) > 5 : echo term verbatim (label=whPM) > 6 : echo term verbatim (label=table) > 7 : echo term verbatim (label=selectArrays) > 8 : echo term verbatim (label=normalizeByReference) > > Error: chunk 8 (label=normalizeByReference) > Error in vsn(xn, lts.quantile = 0.95, subsample = 2e+05, verbose = > verbose) So it looks like the R code in the vignette you are building is raising an error. It might be easier to debug by generating the R files using Rtangle and then stepping through the resulting R code. + seth

Wolfgand, > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "grid" "tools" "methods" "stats" "graphics" "grDevices" "utils" [9] "datasets" "base" other attached packages: davidTiling GO tilingArray pixmap geneplotter annotate genefilter survival "1.0.4" "1.14.1" "1.12.0" "0.4-5" "1.12.0" "1.12.1" "1.12.0" "2.29" vsn strucchange sandwich zoo RColorBrewer affy affyio Biobase "1.12.0" "1.3-1" "2.0-1" "1.2-1" "0.2-3" "1.12.2" "1.2.0" "1.12.2" > Thanks, Lana ----- Original Message ----- From: "Wolfgang Huber" <huber@ebi.ac.uk> To: "Lana Schaffer" <schaffer at="" scripps.edu=""> Cc: <bioconductor at="" stat.math.ethz.ch=""> Sent: Wednesday, January 03, 2007 12:50 PM Subject: Re: [BioC] .Rnw file > > Dear Lana, > what is the output of "sessionInfo()"? > Best wishes > Wolfgang > > > Lana Schaffer wrote: >> Steffen, >>> Sweave("assessNorm.Rnw") >>> Sweave("assessNorm.Rnw") >> Writing to file assessNorm.tex >> Processing code chunks ... >> 1 : echo term hide (label=load) >> 2 : term verbatim (label=errorReporting) >> 3 : echo term verbatim (label=showDavidTilingData) >> 4 : echo term verbatim (label=probeAnno) >> 5 : echo term verbatim (label=whPM) >> 6 : echo term verbatim (label=table) >> 7 : echo term verbatim (label=selectArrays) >> 8 : echo term verbatim (label=normalizeByReference) >> >> Error: chunk 8 (label=normalizeByReference) >> Error in vsn(xn, lts.quantile = 0.95, subsample = 2e+05, verbose = >> verbose) : >> >> The likelihood optimization did not converge. A likely reason is that the >> normalization parameters are not uniquely identifiable from the provided >> data. >> Possibly, the columns of the data matrix are exactly co-linear or affine >> dependent - please verify the data to make sure there were no mix- ups. >> >> Enter a frame number, or 0 to exit >> >> 1: Sweave("assessNorm.Rnw") >> 2: driver$runcode(drobj, chunk, chunkopts) >> 3: RweaveTryStop(err, options) >> >> ----- Original Message ----- >> From: "Steffen Durinck" <durincks at="" mail.nih.gov=""> >> To: "Lana Schaffer" <schaffer at="" scripps.edu=""> >> Cc: <bioconductor at="" stat.math.ethz.ch=""> >> Sent: Wednesday, January 03, 2007 10:55 AM >> Subject: Re: [BioC] .Rnw file >> >> >>> Hi Lana, >>> >>> Try: >>> >>> Sweave("assessNorm.Rnw") >>> >>> best, >>> Steffen >>> >>> Lana Schaffer wrote: >>>> Hi, >>>> I am a little confused how to use the .Rnw file to make a vignette. >>>> Instructions say "source file inst/scripts/assessNorm.Rnw" >>>> but when I use the command : source("assessNorm.Rnw") >>>> I get an error: >>>> Error in parse(file, n = -1, NULL, "?") : syntax error at >>>> 1: %\VignetteIndexEntry{tilingArray - assess normalization} >>>> >>>> probably because it is not an R file. >>>> Would you straighten me out a bit? >>>> >>>> Lana Schaffer >>>> Biostatistics/Informatics >>>> The Scripps Research Institute >>>> DNA Array Core Facility >>>> La Jolla, CA 92037 >>>> (858) 784-2263 >>>> (858) 784-2994 >>>> schaffer at scripps.edu >>>> >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >

Hi Lana, Try: Sweave("assessNorm.Rnw") best, Steffen Lana Schaffer wrote: > Hi, > I am a little confused how to use the .Rnw file to make a vignette. > Instructions say "source file inst/scripts/assessNorm.Rnw" > but when I use the command : source("assessNorm.Rnw") > I get an error: > Error in parse(file, n = -1, NULL, "?") : syntax error at > 1: %\VignetteIndexEntry{tilingArray - assess normalization} > > probably because it is not an R file. > Would you straighten me out a bit? > > Lana Schaffer > Biostatistics/Informatics > The Scripps Research Institute > DNA Array Core Facility > La Jolla, CA 92037 > (858) 784-2263 > (858) 784-2994 > schaffer at scripps.edu > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Wolfgang, > Can you please try with tilingArray from the development branch > http://www.bioconductor.org/packages/2.0/bioc/html/tilingArray.html > and see if you can reproduce this? Warning message: package 'tilingArray' was built under R version 2.5.0 Error: chunk 8 (label=normalizeByReference) Error in vsn(xn, lts.quantile = 0.95, subsample = 2e+05, verbose = verbose) : The likelihood optimization did not converge. A likely reason is that the normalization parameters are not uniquely identifiable from the provided data. Possibly, the columns of the data matrix are exactly co-linear or affine dependent - please verify the data to make sure there were no mix-ups. Enter a frame number, or 0 to exit 1: Sweave("assessNorm.Rnw") 2: driver$runcode(drobj, chunk, chunkopts) 3: RweaveTryStop(err, options) Lana ----- Original Message ----- From: "Wolfgang Huber" <huber@ebi.ac.uk> To: "Lana Schaffer" <schaffer at="" scripps.edu=""> Cc: <bioconductor at="" stat.math.ethz.ch=""> Sent: Wednesday, January 03, 2007 4:11 PM Subject: Re: [BioC] .Rnw file > Dear Lana, > > Can you please try with tilingArray from the development branch > http://www.bioconductor.org/packages/2.0/bioc/html/tilingArray.html > and see if you can reproduce this? > > I have no idea what could cause your problem reported below, and have not > seen it before (however I have never used the Windows-version of R for > this). > > Has anyone else seen this error for these data? > > Best wishes > Wolfgang > > > >> Wolfgand, >>> sessionInfo() >> R version 2.4.0 (2006-10-03) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] "splines" "grid" "tools" "methods" "stats" >> "graphics" "grDevices" "utils" >> [9] "datasets" "base" >> >> other attached packages: >> davidTiling GO tilingArray pixmap geneplotter annotate >> genefilter survival >> "1.0.4" "1.14.1" "1.12.0" "0.4-5" "1.12.0" "1.12.1" >> "1.12.0" "2.29" >> vsn strucchange sandwich zoo RColorBrewer affy >> affyio Biobase >> "1.12.0" "1.3-1" "2.0-1" "1.2-1" "0.2-3" "1.12.2" >> "1.2.0" "1.12.2" >>> >> Thanks, >> Lana >> ----- Original Message ----- From: "Wolfgang Huber" <huber at="" ebi.ac.uk=""> >> To: "Lana Schaffer" <schaffer at="" scripps.edu=""> >> Cc: <bioconductor at="" stat.math.ethz.ch=""> >> Sent: Wednesday, January 03, 2007 12:50 PM >> Subject: Re: [BioC] .Rnw file >> >> >>> >>> Dear Lana, >>> what is the output of "sessionInfo()"? >>> Best wishes >>> Wolfgang >>> >>> >>> Lana Schaffer wrote: >>>> Steffen, >>>>> Sweave("assessNorm.Rnw") >>>>> Sweave("assessNorm.Rnw") >>>> Writing to file assessNorm.tex >>>> Processing code chunks ... >>>> 1 : echo term hide (label=load) >>>> 2 : term verbatim (label=errorReporting) >>>> 3 : echo term verbatim (label=showDavidTilingData) >>>> 4 : echo term verbatim (label=probeAnno) >>>> 5 : echo term verbatim (label=whPM) >>>> 6 : echo term verbatim (label=table) >>>> 7 : echo term verbatim (label=selectArrays) >>>> 8 : echo term verbatim (label=normalizeByReference) >>>> >>>> Error: chunk 8 (label=normalizeByReference) >>>> Error in vsn(xn, lts.quantile = 0.95, subsample = 2e+05, verbose = >>>> verbose) : >>>> >>>> The likelihood optimization did not converge. A likely reason is that >>>> the normalization parameters are not uniquely identifiable from the >>>> provided data. >>>> Possibly, the columns of the data matrix are exactly co-linear or >>>> affine dependent - please verify the data to make sure there were no >>>> mix-ups. >>>> >>>> Enter a frame number, or 0 to exit >>>> >>>> 1: Sweave("assessNorm.Rnw") >>>> 2: driver$runcode(drobj, chunk, chunkopts) >>>> 3: RweaveTryStop(err, options) >>>> >>>> ----- Original Message ----- From: "Steffen Durinck" >>>> <durincks at="" mail.nih.gov=""> >>>> To: "Lana Schaffer" <schaffer at="" scripps.edu=""> >>>> Cc: <bioconductor at="" stat.math.ethz.ch=""> >>>> Sent: Wednesday, January 03, 2007 10:55 AM >>>> Subject: Re: [BioC] .Rnw file >>>> >>>> >>>>> Hi Lana, >>>>> >>>>> Try: >>>>> >>>>> Sweave("assessNorm.Rnw") >>>>> >>>>> best, >>>>> Steffen >>>>> >>>>> Lana Schaffer wrote: >>>>>> Hi, >>>>>> I am a little confused how to use the .Rnw file to make a vignette. >>>>>> Instructions say "source file inst/scripts/assessNorm.Rnw" >>>>>> but when I use the command : source("assessNorm.Rnw") >>>>>> I get an error: >>>>>> Error in parse(file, n = -1, NULL, "?") : syntax error at >>>>>> 1: %\VignetteIndexEntry{tilingArray - assess normalization} >>>>>> >>>>>> probably because it is not an R file. >>>>>> Would you straighten me out a bit? >>>>>> >>>>>> Lana Schaffer >>>>>> Biostatistics/Informatics >>>>>> The Scripps Research Institute >>>>>> DNA Array Core Facility >>>>>> La Jolla, CA 92037 >>>>>> (858) 784-2263 >>>>>> (858) 784-2994 >>>>>> schaffer at scripps.edu >>>>>> >>>>>> >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>> -- >>> ------------------------------------------------------------------ >>> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>> > > > -- > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >