Search
Question: make.cdf.package Error in copySubstitute
0
gravatar for matthew vitalone
3.7 years ago by
matthew vitalone30 wrote:
Hi, I am trying to create a cdf package to analyise a set of Affy HTA2.0 arrays, which don't have one yet. I have followed the documentation, but I get this message: Creating package in C:/Matthew/Sen vs. non-Sen/HTA data/HTA-2_0.r1.Psrs_mps Error in copySubstitute(dir(originDir, full.names = TRUE), pkgdir, symbolValues, : 'symbolValues' must only contain characters. I'm not sure where to go next. I'm not sure how to fix this as this function is called by biobase, which is called by make.cdf.package function. All I need is this package to move forward in the analysis. Here are the details of my session. R3.0.2 in RStudio ################## library(limma)library(gcrma) Loading required package: affy Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from 'package:limma': plotMA The following object is masked from 'package:stats': xtabs The following objects are masked from 'package:base': anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > setwd("C:/Matthew/Sen vs. non-Sen/HTA data") > targets <- readTargets("targets.txt") > View(targets) > ab <- ReadAffy(filenames=targets$FileName) > eset <- gcrma(ab) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HTA-2_0 Library - package hta20cdf not installed Bioconductor - hta20cdf not available ##Trying to create cdf package ## Contacted Affymetrix and downloaded their CDF file for these arrays source("http://bioconductor.org/biocLite.R")Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for helpbiocLite("makecdfenv")BioC_mirror: http://bioconductor.orgUsing Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.Installing package(s) 'makecdfenv'trying URL 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/ma kecdfenv_1.38.0.zip'Content type 'application/zip' length 3373763 bytes (3.2 Mb)opened URLdownloaded 3.2 Mb package 'makecdfenv' successfully unpacked and MD5 sums checked make.cdf.package("HTA-2_0.r1.Psrs_mps.cdf",+ packagename = "HTA-2_0.r1.Psrs_mps",+ cdf.path = getwd(),+ package.path = getwd(),+ compress = FALSE,+ author = "The Bioconductor Project",+ maintainer = "Biocore Data Team <biocannotation@lists.fhcrc.org>",+ version = packageDescription("makecdfenv", fields ="1.0"),+ species = "Homo_sapiens",+ unlink = TRUE,+ verbose = TRUE)Reading CDF file. Creating CDF environment Wait for about 681 dots.................................................................. ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ................................................ Creating package in C:/Matthew/Sen vs. non-Sen/HTA data/HTA-2_0.r1.Psrs_mps Error in copySubstitute(dir(originDir, full.names = TRUE), pkgdir, symbolValues, : 'symbolValues' must only contain characters. Thanks, Matthew [[alternative HTML version deleted]]
ADD COMMENTlink modified 3.7 years ago by James W. MacDonald45k • written 3.7 years ago by matthew vitalone30
0
gravatar for James W. MacDonald
3.7 years ago by
United States
James W. MacDonald45k wrote:
Hi Matthew, You cannot use the makecdfenv/affy analysis pipeline for this array. You can use pdInfoBuilder/oligo, and presumably xps (although Christian Stratowa will know for sure about that). Note that the infrastructure for pdInfoBuilder and oligo have recently been added, so you will need to use R-devel to get the functionality. Also see this: https://stat.ethz.ch/pipermail/bioconductor/attachments/20140208/f885a 15d/attachment.pl And note that there are no (to my knowledge) HTA specific analysis packages in BioC, so if you want to do something similar to what Affy's TAC software does, you will have to roll your own. Best, Jim On 3/25/2014 7:06 PM, matthew vitalone wrote: > Hi, > > I am trying to create a cdf package to analyise a set of Affy HTA2.0 > arrays, which don't have one yet. I have followed the documentation, but I > get this message: > > Creating package in C:/Matthew/Sen vs. non-Sen/HTA > data/HTA-2_0.r1.Psrs_mps Error in copySubstitute(dir(originDir, > full.names = TRUE), pkgdir, symbolValues, : > 'symbolValues' must only contain characters. > > I'm not sure where to go next. I'm not sure how to fix this as this > function is called by biobase, which is called by make.cdf.package > function. All I need is this package to move forward in the analysis. > > Here are the details of my session. R3.0.2 in RStudio > > > > ################## > > library(limma)library(gcrma) > > > Loading required package: affy Loading required package: BiocGenerics Loading > required package: parallel Attaching package: 'BiocGenerics' The following > objects are masked from 'package:parallel': clusterApply, clusterApplyLB, > clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, > parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following > object is masked from 'package:limma': plotMA The following object is > masked from 'package:stats': xtabs The following objects are masked from > 'package:base': anyDuplicated, append, as.data.frame, as.vector, cbind, > colnames, duplicated, eval, evalq, Filter, Find, get, intersect, > is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, > pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, > setdiff, sort, table, tapply, union, unique, unlist Loading required > package: Biobase Welcome to Bioconductor Vignettes contain introductory > material; view with 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > > setwd("C:/Matthew/Sen > vs. non-Sen/HTA data") > targets <- readTargets("targets.txt") > View(targets) >> ab <- ReadAffy(filenames=targets$FileName) > eset <- gcrma(ab) Error in > getCdfInfo(object) : Could not obtain CDF environment, problems > encountered: Specified environment does not contain HTA-2_0 Library - > package hta20cdf not installed Bioconductor - hta20cdf not available > > > > ##Trying to create cdf package > ## Contacted Affymetrix and downloaded their CDF file for these arrays > > source("http://bioconductor.org/biocLite.R")Bioconductor version 2.13 > (BiocInstaller 1.12.0), ?biocLite for > helpbiocLite("makecdfenv")BioC_mirror: http://bioconductor.orgUsing > Bioconductor version 2.13 (BiocInstaller 1.12.0), R version > 3.0.2.Installing package(s) 'makecdfenv'trying URL > 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0/ makecdfenv_1.38.0.zip'Content > type 'application/zip' length 3373763 bytes (3.2 Mb)opened > URLdownloaded 3.2 Mb > package 'makecdfenv' successfully unpacked and MD5 sums checked > > > > make.cdf.package("HTA-2_0.r1.Psrs_mps.cdf",+ > packagename = "HTA-2_0.r1.Psrs_mps",+ cdf.path = > getwd(),+ package.path = getwd(),+ > compress = FALSE,+ author = "The Bioconductor > Project",+ maintainer = "Biocore Data Team > <biocannotation at="" lists.fhcrc.org="">",+ version = > packageDescription("makecdfenv", fields ="1.0"),+ > species = "Homo_sapiens",+ unlink = TRUE,+ > verbose = TRUE)Reading CDF file. > Creating CDF environment > Wait for about 681 > dots................................................................ ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... .................................................. > Creating package in C:/Matthew/Sen vs. non-Sen/HTA > data/HTA-2_0.r1.Psrs_mps Error in copySubstitute(dir(originDir, > full.names = TRUE), pkgdir, symbolValues, : > 'symbolValues' must only contain characters. > > > Thanks, > Matthew > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 3.7 years ago by James W. MacDonald45k
Dear Matthhew, Please note that the HTA 2.0 arry is an array which is not supported by package 'xps'. The reason is that it contains completely different annotation files, for which Affymetrix did not supply README files. Best regards, Christian On 3/26/14 2:25 PM, James W. MacDonald wrote: > Hi Matthew, > > You cannot use the makecdfenv/affy analysis pipeline for this array. > > You can use pdInfoBuilder/oligo, and presumably xps (although Christian > Stratowa will know for sure about that). Note that the infrastructure > for pdInfoBuilder and oligo have recently been added, so you will need > to use R-devel to get the functionality. Also see this: > > https://stat.ethz.ch/pipermail/bioconductor/attachments/20140208/f88 5a15d/attachment.pl > > > And note that there are no (to my knowledge) HTA specific analysis > packages in BioC, so if you want to do something similar to what Affy's > TAC software does, you will have to roll your own. > > Best, > > Jim > > > On 3/25/2014 7:06 PM, matthew vitalone wrote: >> Hi, >> >> I am trying to create a cdf package to analyise a set of Affy HTA2.0 >> arrays, which don't have one yet. I have followed the documentation, >> but I >> get this message: >> >> Creating package in C:/Matthew/Sen vs. non-Sen/HTA >> data/HTA-2_0.r1.Psrs_mps Error in copySubstitute(dir(originDir, >> full.names = TRUE), pkgdir, symbolValues, : >> 'symbolValues' must only contain characters. >> >> I'm not sure where to go next. I'm not sure how to fix this as this >> function is called by biobase, which is called by make.cdf.package >> function. All I need is this package to move forward in the analysis. >> >> Here are the details of my session. R3.0.2 in RStudio >> >> >> >> ################## >> >> library(limma)library(gcrma) >> >> >> Loading required package: affy Loading required package: BiocGenerics >> Loading >> required package: parallel Attaching package: 'BiocGenerics' The >> following >> objects are masked from 'package:parallel': clusterApply, clusterApplyLB, >> clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, >> parCapply, >> parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following >> object is masked from 'package:limma': plotMA The following object is >> masked from 'package:stats': xtabs The following objects are masked from >> 'package:base': anyDuplicated, append, as.data.frame, as.vector, cbind, >> colnames, duplicated, eval, evalq, Filter, Find, get, intersect, >> is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, >> pmax.int, >> pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, >> setdiff, sort, table, tapply, union, unique, unlist Loading required >> package: Biobase Welcome to Bioconductor Vignettes contain introductory >> material; view with 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")', and for packages 'citation("pkgname")'. > >> setwd("C:/Matthew/Sen >> vs. non-Sen/HTA data") > targets <- readTargets("targets.txt") > >> View(targets) >>> ab <- ReadAffy(filenames=targets$FileName) > eset <- gcrma(ab) Error in >> getCdfInfo(object) : Could not obtain CDF environment, problems >> encountered: Specified environment does not contain HTA-2_0 Library - >> package hta20cdf not installed Bioconductor - hta20cdf not available >> >> >> >> ##Trying to create cdf package >> ## Contacted Affymetrix and downloaded their CDF file for these arrays >> >> source("http://bioconductor.org/biocLite.R")Bioconductor version 2.13 >> (BiocInstaller 1.12.0), ?biocLite for >> helpbiocLite("makecdfenv")BioC_mirror: http://bioconductor.orgUsing >> Bioconductor version 2.13 (BiocInstaller 1.12.0), R version >> 3.0.2.Installing package(s) 'makecdfenv'trying URL >> 'http://bioconductor.org/packages/2.13/bioc/bin/windows/contrib/3.0 /makecdfenv_1.38.0.zip'Content >> >> type 'application/zip' length 3373763 bytes (3.2 Mb)opened >> URLdownloaded 3.2 Mb >> package 'makecdfenv' successfully unpacked and MD5 sums checked >> >> >> >> make.cdf.package("HTA-2_0.r1.Psrs_mps.cdf",+ >> packagename = "HTA-2_0.r1.Psrs_mps",+ cdf.path = >> getwd(),+ package.path = getwd(),+ >> compress = FALSE,+ author = "The Bioconductor >> Project",+ maintainer = "Biocore Data Team >> <biocannotation at="" lists.fhcrc.org="">",+ version = >> packageDescription("makecdfenv", fields ="1.0"),+ >> species = "Homo_sapiens",+ unlink = TRUE,+ >> verbose = TRUE)Reading CDF file. >> Creating CDF environment >> Wait for about 681 >> dots............................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ...................................................................... ................................................... >> >> Creating package in C:/Matthew/Sen vs. non-Sen/HTA >> data/HTA-2_0.r1.Psrs_mps Error in copySubstitute(dir(originDir, >> full.names = TRUE), pkgdir, symbolValues, : >> 'symbolValues' must only contain characters. >> >> >> Thanks, >> Matthew >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >
ADD REPLYlink written 3.7 years ago by cstrato3.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 103 users visited in the last hour