Hi I have multiple pair files from a Nimblegen methylation array that I have converted to XYS files. I am trying to feed them into pdInfobuilder using the script below, but it crashes out with the following error: Error in validObject(.Object) : invalid class ???ScalarCharacter??? object: ScalarCharacter must have length one Does this mean that pdInfobuilder can only take one file at a time? I thought that as the file was being read into an array it could analyse multiple files Thanks Andrew library(pdInfoBuilder) baseDir <- "/mnt/cdrive/Nimblegen/methylationpercentages" ndf <- list.files(baseDir, pattern = ".ndf",full.names = TRUE) xys <- list.files(baseDir, pattern = ".xys",full.names = TRUE) pos <- list.files(baseDir, pattern = ".pos",full.names = TRUE) seed <- new("NgsTilingPDInfoPkgSeed",ndfFile = ndf, xysFile = xys, posFile = pos, author = "Andrew Beggs", email = "a.beggs at bham.ac.uk", biocViews = "AnnotationData",genomebuild = "HG 18", organism = "Human", species = "Homo Sapiens", url = "http://www.biostat.jhsph.edu/~bcarvalh") makePdInfoPackage(seed, destDir = ".") -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.22.0 oligo_1.22.0 oligoClasses_1.20.0 [4] affxparser_1.30.0 RSQLite_0.11.2 DBI_0.2-5 [7] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 [4] bit_1.1-9 codetools_0.2-8 ff_2.2-9 [7] foreach_1.4.0 GenomicRanges_1.10.3 IRanges_1.16.3 [10] iterators_1.0.6 parallel_2.15.2 preprocessCore_1.20.0 [13] splines_2.15.2 stats4_2.15.2 tools_2.15.2 [16] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

Can't answer in details, but you pass on leave 1 of your files, not all. b Sent from a mobile device. Please apologise for brevity, spelling and punctuation. "Andrew Beggs [guest]" <guest@bioconductor.org> wrote: Hi I have multiple pair files from a Nimblegen methylation array that I have converted to XYS files. I am trying to feed them into pdInfobuilder using the script below, but it crashes out with the following error: Error in validObject(.Object) : invalid class “ScalarCharacter” object: ScalarCharacter must have length one Does this mean that pdInfobuilder can only take one file at a time? I thought that as the file was being read into an array it could analyse multiple files Thanks Andrew library(pdInfoBuilder) baseDir <- "/mnt/cdrive/Nimblegen/methylationpercentages" ndf <- list.files(baseDir, pattern = ".ndf",full.names = TRUE) xys <- list.files(baseDir, pattern = ".xys",full.names = TRUE) pos <- list.files(baseDir, pattern = ".pos",full.names = TRUE) seed <- new("NgsTilingPDInfoPkgSeed",ndfFile = ndf, xysFile = xys, posFile = pos, author = "Andrew Beggs", email = "a.beggs@bham.ac.uk", biocViews = "AnnotationData",genomebuild = "HG 18", organism = "Human", species = "Homo Sapiens", url = "http://www.biostat.jhsph.edu/~bcarvalh") makePdInfoPackage(seed, destDir = ".") -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.22.0 oligo_1.22.0 oligoClasses_1.20.0 [4] affxparser_1.30.0 RSQLite_0.11.2 DBI_0.2-5 [7] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 [4] bit_1.1-9 codetools_0.2-8 ff_2.2-9 [7] foreach_1.4.0 GenomicRanges_1.10.3 IRanges_1.16.3 [10] iterators_1.0.6 parallel_2.15.2 preprocessCore_1.20.0 [13] splines_2.15.2 stats4_2.15.2 tools_2.15.2 [16] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org. NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above- named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. [[alternative HTML version deleted]]

So I pass on the path rather than the file name? A From: Benilton Carvalho [mailto:Benilton.Carvalho@cancer.org.uk] Sent: 31 October 2012 13:11 To: guest@bioconductor.org; bioconductor@r-project.org; a.beggs@bham.ac.uk Cc: Benilton Carvalho Subject: Re: Passing multiple files to pdInfobuilder Can't answer in details, but you pass on leave 1 of your files, not all. b Sent from a mobile device. Please apologise for brevity, spelling and punctuation. "Andrew Beggs [guest]" <guest@bioconductor.org<mailto:guest@bioconductor.org>> wrote: Hi I have multiple pair files from a Nimblegen methylation array that I have converted to XYS files. I am trying to feed them into pdInfobuilder using the script below, but it crashes out with the following error: Error in validObject(.Object) : invalid class “ScalarCharacter” object: ScalarCharacter must have length one Does this mean that pdInfobuilder can only take one file at a time? I thought that as the file was being read into an array it could analyse multiple files Thanks Andrew library(pdInfoBuilder) baseDir <- "/mnt/cdrive/Nimblegen/methylationpercentages" ndf <- list.files(baseDir, pattern = ".ndf",full.names = TRUE) xys <- list.files(baseDir, pattern = ".xys",full.names = TRUE) pos <- list.files(baseDir, pattern = ".pos",full.names = TRUE) seed <- new("NgsTilingPDInfoPkgSeed",ndfFile = ndf, xysFile = xys, posFile = pos, author = "Andrew Beggs", email = "a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk>", biocViews = "AnnotationData",genomebuild = "HG 18", organism = "Human", species = "Homo Sapiens", url = "http://www.biostat.jhsph.edu/~bcarvalh") makePdInfoPackage(seed, destDir = ".") -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.22.0 oligo_1.22.0 oligoClasses_1.20.0 [4] affxparser_1.30.0 RSQLite_0.11.2 DBI_0.2-5 [7] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 [4] bit_1.1-9 codetools_0.2-8 ff_2.2-9 [7] foreach_1.4.0 GenomicRanges_1.10.3 IRanges_1.16.3 [10] iterators_1.0.6 parallel_2.15.2 preprocessCore_1.20.0 [13] splines_2.15.2 stats4_2.15.2 tools_2.15.2 [16] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org. NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above- named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. [[alternative HTML version deleted]]

Auto correct problem, sorry. You should pass only 1 of your xys files. All that the builder needs is 1 xys as a template. Sent from a mobile device. Please apologise for brevity, spelling and punctuation. Benilton Carvalho <benilton.carvalho@cancer.org.uk> wrote: Can't answer in details, but you pass on leave 1 of your files, not all. b Sent from a mobile device. Please apologise for brevity, spelling and punctuation. "Andrew Beggs [guest]" <guest@bioconductor.org> wrote: Hi I have multiple pair files from a Nimblegen methylation array that I have converted to XYS files. I am trying to feed them into pdInfobuilder using the script below, but it crashes out with the following error: Error in validObject(.Object) : invalid class “ScalarCharacter” object: ScalarCharacter must have length one Does this mean that pdInfobuilder can only take one file at a time? I thought that as the file was being read into an array it could analyse multiple files Thanks Andrew library(pdInfoBuilder) baseDir <- "/mnt/cdrive/Nimblegen/methylationpercentages" ndf <- list.files(baseDir, pattern = ".ndf",full.names = TRUE) xys <- list.files(baseDir, pattern = ".xys",full.names = TRUE) pos <- list.files(baseDir, pattern = ".pos",full.names = TRUE) seed <- new("NgsTilingPDInfoPkgSeed",ndfFile = ndf, xysFile = xys, posFile = pos, author = "Andrew Beggs", email = "a.beggs@bham.ac.uk", biocViews = "AnnotationData",genomebuild = "HG 18", organism = "Human", species = "Homo Sapiens", url = "http://www.biostat.jhsph.edu/~bcarvalh") makePdInfoPackage(seed, destDir = ".") -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.22.0 oligo_1.22.0 oligoClasses_1.20.0 [4] affxparser_1.30.0 RSQLite_0.11.2 DBI_0.2-5 [7] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 [4] bit_1.1-9 codetools_0.2-8 ff_2.2-9 [7] foreach_1.4.0 GenomicRanges_1.10.3 IRanges_1.16.3 [10] iterators_1.0.6 parallel_2.15.2 preprocessCore_1.20.0 [13] splines_2.15.2 stats4_2.15.2 tools_2.15.2 [16] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org. NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above- named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. [[alternative HTML version deleted]]

Of course, sorry I was being stupid A From: Benilton Carvalho [mailto:Benilton.Carvalho@cancer.org.uk] Sent: 31 October 2012 13:39 To: Benilton Carvalho; guest@bioconductor.org; bioconductor@r-project.org; a.beggs@bham.ac.uk Cc: Benilton Carvalho Subject: Re: Passing multiple files to pdInfobuilder Auto correct problem, sorry. You should pass only 1 of your xys files. All that the builder needs is 1 xys as a template. Sent from a mobile device. Please apologise for brevity, spelling and punctuation. Benilton Carvalho <benilton.carvalho@cancer.org.uk<mailto:benilton.car valho@cancer.org.uk="">> wrote: Can't answer in details, but you pass on leave 1 of your files, not all. b Sent from a mobile device. Please apologise for brevity, spelling and punctuation. "Andrew Beggs [guest]" <guest@bioconductor.org<mailto:guest@bioconductor.org>> wrote: Hi I have multiple pair files from a Nimblegen methylation array that I have converted to XYS files. I am trying to feed them into pdInfobuilder using the script below, but it crashes out with the following error: Error in validObject(.Object) : invalid class “ScalarCharacter” object: ScalarCharacter must have length one Does this mean that pdInfobuilder can only take one file at a time? I thought that as the file was being read into an array it could analyse multiple files Thanks Andrew library(pdInfoBuilder) baseDir <- "/mnt/cdrive/Nimblegen/methylationpercentages" ndf <- list.files(baseDir, pattern = ".ndf",full.names = TRUE) xys <- list.files(baseDir, pattern = ".xys",full.names = TRUE) pos <- list.files(baseDir, pattern = ".pos",full.names = TRUE) seed <- new("NgsTilingPDInfoPkgSeed",ndfFile = ndf, xysFile = xys, posFile = pos, author = "Andrew Beggs", email = "a.beggs@bham.ac.uk<mailto:a.beggs@bham.ac.uk>", biocViews = "AnnotationData",genomebuild = "HG 18", organism = "Human", species = "Homo Sapiens", url = "http://www.biostat.jhsph.edu/~bcarvalh") makePdInfoPackage(seed, destDir = ".") -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.22.0 oligo_1.22.0 oligoClasses_1.20.0 [4] affxparser_1.30.0 RSQLite_0.11.2 DBI_0.2-5 [7] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 Biostrings_2.26.2 [4] bit_1.1-9 codetools_0.2-8 ff_2.2-9 [7] foreach_1.4.0 GenomicRanges_1.10.3 IRanges_1.16.3 [10] iterators_1.0.6 parallel_2.15.2 preprocessCore_1.20.0 [13] splines_2.15.2 stats4_2.15.2 tools_2.15.2 [16] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org. NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above- named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. [[alternative HTML version deleted]]