Question: PdInfoBuilder for nimblegen array
0
gravatar for Alex Rodriguez
9.7 years ago by
Alex Rodriguez40 wrote:
Hi, I am new using pdInfoBuilder, so I may be missing something. I am trying to use pdInfoBuilder to make an annotation package. However, I get an error after the makePdInfoPackage(seed, destDir = "./") command. Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate Has anybody encountered this message? Thanks!, Alex Here is my list of commands: > library(pdInfoBuilder) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: RSQLite Loading required package: DBI Loading required package: affxparser Loading required package: oligo Loading required package: oligoClasses Loading required package: preprocessCore Welcome to oligo version 1.10.2 > baseDir <- "/cchome/qichen2/Nimblegen_methylation/21863" > (ndf <- list.files(baseDir, pattern = "ndf", full.names = TRUE)) [1] "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_MeDI P_HX1. ndf" > (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1]) [1] "/cchome/qichen2/Nimblegen_methylation/21863/38693602_532.xys" > (pos <- list.files(baseDir, pattern = ".pos", full.names = TRUE)) [1] "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_MeDI P_HX1. pos" > seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = xys,posFile = pos, author = "AR", biocViews = "AnnotationData", genomebuild = "HG 18", organism = "Human", species = "Homo Sapiens") > makePdInfoPackage(seed, destDir = "./") ====================================================================== ====== ==== Building annotation package for Nimblegen Tiling Array NDF: 081229_HG18_Promoter_MeDIP_HX1.ndf POS: 081229_HG18_Promoter_MeDIP_HX1.pos XYS: 38693602_532.xys ====================================================================== ====== ==== Parsing file: 081229_HG18_Promoter_MeDIP_HX1.ndf ... OK Parsing file: 081229_HG18_Promoter_MeDIP_HX1.pos ... OK Merging NDF and POS files... OK Parsing file: 38693602_532.xys ... OK Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate Calls: makePdInfoPackage ... aggregate -> aggregate.default -> aggregate.data.frame In addition: Warning message: In is.na(ndfdata[["SIGNAL"]]) : is.na() applied to non-(list or vector) of type 'NULL' Execution halted This email is intended only for the use of the individua...{{dropped:6}}
ADD COMMENTlink modified 9.7 years ago by Benilton Carvalho4.3k • written 9.7 years ago by Alex Rodriguez40
Answer: PdInfoBuilder for nimblegen array
0
gravatar for Benilton Carvalho
9.7 years ago by
Brazil/Campinas/UNICAMP
Benilton Carvalho4.3k wrote:
Hi Alex, what's your sessionInfo()? Additionally, can you confirm you got the XYS files from NimbleGen or NimbleScan? Thank you, benilton On Fri, Feb 19, 2010 at 7:44 PM, Alex Rodriguez <arodrigu1 at="" bsd.uchicago.edu=""> wrote: > Hi, > I am new using pdInfoBuilder, so I may be missing something. I am trying to > use pdInfoBuilder to make an annotation package. However, I get an error > after the makePdInfoPackage(seed, destDir = "./") command. > > Error in aggregate.data.frame(as.data.frame(x), ...) : > ?no rows to aggregate > > ?Has anybody encountered this message? > > Thanks!, > > Alex > > Here is my list of commands: > >> library(pdInfoBuilder) > Loading required package: Biobase > > Welcome to Bioconductor > > ?Vignettes contain introductory material. To view, type > ?'openVignette()'. To cite Bioconductor, see > ?'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: RSQLite > Loading required package: DBI > Loading required package: affxparser > Loading required package: oligo > Loading required package: oligoClasses > Loading required package: preprocessCore > Welcome to oligo version 1.10.2 >> baseDir <- "/cchome/qichen2/Nimblegen_methylation/21863" >> (ndf <- list.files(baseDir, pattern = "ndf", full.names = TRUE)) > [1] > "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_Me DIP_HX1. > ndf" >> (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1]) > [1] "/cchome/qichen2/Nimblegen_methylation/21863/38693602_532.xys" >> (pos <- list.files(baseDir, pattern = ".pos", full.names = TRUE)) > [1] > "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_Me DIP_HX1. > pos" >> seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = xys,posFile = > pos, author = "AR", biocViews > = "AnnotationData", genomebuild = "HG 18", organism = "Human", species = > "Homo Sapiens") >> makePdInfoPackage(seed, destDir = "./") > ==================================================================== ======== > ==== > Building annotation package for Nimblegen Tiling Array > NDF: ?081229_HG18_Promoter_MeDIP_HX1.ndf > POS: ?081229_HG18_Promoter_MeDIP_HX1.pos > XYS: ?38693602_532.xys > ==================================================================== ======== > ==== > Parsing file: 081229_HG18_Promoter_MeDIP_HX1.ndf ... OK > Parsing file: 081229_HG18_Promoter_MeDIP_HX1.pos ... OK > Merging NDF and POS files... OK > Parsing file: 38693602_532.xys ... OK > Error in aggregate.data.frame(as.data.frame(x), ...) : > ?no rows to aggregate > Calls: makePdInfoPackage ... aggregate -> aggregate.default -> > aggregate.data.frame > In addition: Warning message: > In is.na(ndfdata[["SIGNAL"]]) : > ?is.na() applied to non-(list or vector) of type 'NULL' > Execution halted > > > > This email is intended only for the use of the individua...{{dropped:6}} > > _______________________________________________ > 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 >
ADD COMMENTlink written 9.7 years ago by Benilton Carvalho4.3k
Hi Benilton, Thanks for your prompt reply! The .xys file were created from .pair file which are from NimbleScan. Here is my output for sessionInfo(): > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu 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=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 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] pdInfoBuilder_1.10.1 oligo_1.10.2 preprocessCore_1.8.0 [4] oligoClasses_1.8.0 affxparser_1.18.0 RSQLite_0.8-2 [7] DBI_0.2-5 Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 Biostrings_2.14.12 IRanges_1.4.11 splines_2.10.1 Thanks for your input! Alex On 2/23/10 4:52 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: > Hi Alex, > > what's your sessionInfo()? > > Additionally, can you confirm you got the XYS files from NimbleGen or > NimbleScan? > > Thank you, > > benilton > > On Fri, Feb 19, 2010 at 7:44 PM, Alex Rodriguez > <arodrigu1 at="" bsd.uchicago.edu=""> wrote: >> Hi, >> I am new using pdInfoBuilder, so I may be missing something. I am trying to >> use pdInfoBuilder to make an annotation package. However, I get an error >> after the makePdInfoPackage(seed, destDir = "./") command. >> >> Error in aggregate.data.frame(as.data.frame(x), ...) : >> ?no rows to aggregate >> >> ?Has anybody encountered this message? >> >> Thanks!, >> >> Alex >> >> Here is my list of commands: >> >>> library(pdInfoBuilder) >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> ?Vignettes contain introductory material. To view, type >> ?'openVignette()'. To cite Bioconductor, see >> ?'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> Loading required package: RSQLite >> Loading required package: DBI >> Loading required package: affxparser >> Loading required package: oligo >> Loading required package: oligoClasses >> Loading required package: preprocessCore >> Welcome to oligo version 1.10.2 >>> baseDir <- "/cchome/qichen2/Nimblegen_methylation/21863" >>> (ndf <- list.files(baseDir, pattern = "ndf", full.names = TRUE)) >> [1] >> "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_M eDIP_HX1. >> ndf" >>> (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1]) >> [1] "/cchome/qichen2/Nimblegen_methylation/21863/38693602_532.xys" >>> (pos <- list.files(baseDir, pattern = ".pos", full.names = TRUE)) >> [1] >> "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_M eDIP_HX1. >> pos" >>> seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = xys,posFile = >> pos, author = "AR", biocViews >> = "AnnotationData", genomebuild = "HG 18", organism = "Human", species = >> "Homo Sapiens") >>> makePdInfoPackage(seed, destDir = "./") >> =================================================================== ========= >> ==== >> Building annotation package for Nimblegen Tiling Array >> NDF: ?081229_HG18_Promoter_MeDIP_HX1.ndf >> POS: ?081229_HG18_Promoter_MeDIP_HX1.pos >> XYS: ?38693602_532.xys >> =================================================================== ========= >> ==== >> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.ndf ... OK >> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.pos ... OK >> Merging NDF and POS files... OK >> Parsing file: 38693602_532.xys ... OK >> Error in aggregate.data.frame(as.data.frame(x), ...) : >> ?no rows to aggregate >> Calls: makePdInfoPackage ... aggregate -> aggregate.default -> >> aggregate.data.frame >> In addition: Warning message: >> In is.na(ndfdata[["SIGNAL"]]) : >> ?is.na() applied to non-(list or vector) of type 'NULL' >> Execution halted >> >> >> >> This email is intended only for the use of the individua...{{dropped:6}} >> >> _______________________________________________ >> 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 >> This email is intended only for the use of the individua...{{dropped:8}}
ADD REPLYlink written 9.7 years ago by Alex Rodriguez40
Hi Alex, So, you're creating the XYS files yourself, right? These files should be sorted by X/Y coordinates and the SIGNAL columns for the control probes should be NA. If you happen to have NimbleScan, it can create the XYS files directly and appropriately. If you're going to create them manually, they should follow the requirements above. Can you tell me if yours are like this? THanks, b On Wed, Feb 24, 2010 at 6:01 PM, Alex Rodriguez <arodrigu1 at="" bsd.uchicago.edu=""> wrote: > Hi Benilton, > Thanks for your prompt reply! > The .xys file were created from .pair file which are from NimbleScan. > > Here is my output for sessionInfo(): > >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-unknown-linux-gnu > > 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=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 > ?[7] LC_PAPER=en_US.UTF-8 ? ? ? 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] pdInfoBuilder_1.10.1 oligo_1.10.2 ? ? ? ? preprocessCore_1.8.0 > [4] oligoClasses_1.8.0 ? affxparser_1.18.0 ? ?RSQLite_0.8-2 > [7] DBI_0.2-5 ? ? ? ? ? ?Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 ? ? ?Biostrings_2.14.12 IRanges_1.4.11 ? ? splines_2.10.1 > > Thanks for your input! > > Alex > > On 2/23/10 4:52 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: > >> Hi Alex, >> >> what's your sessionInfo()? >> >> Additionally, can you confirm you got the XYS files from NimbleGen or >> NimbleScan? >> >> Thank you, >> >> benilton >> >> On Fri, Feb 19, 2010 at 7:44 PM, Alex Rodriguez >> <arodrigu1 at="" bsd.uchicago.edu=""> wrote: >>> Hi, >>> I am new using pdInfoBuilder, so I may be missing something. I am trying to >>> use pdInfoBuilder to make an annotation package. However, I get an error >>> after the makePdInfoPackage(seed, destDir = "./") command. >>> >>> Error in aggregate.data.frame(as.data.frame(x), ...) : >>> ?no rows to aggregate >>> >>> ?Has anybody encountered this message? >>> >>> Thanks!, >>> >>> Alex >>> >>> Here is my list of commands: >>> >>>> library(pdInfoBuilder) >>> Loading required package: Biobase >>> >>> Welcome to Bioconductor >>> >>> ?Vignettes contain introductory material. To view, type >>> ?'openVignette()'. To cite Bioconductor, see >>> ?'citation("Biobase")' and for packages 'citation(pkgname)'. >>> >>> Loading required package: RSQLite >>> Loading required package: DBI >>> Loading required package: affxparser >>> Loading required package: oligo >>> Loading required package: oligoClasses >>> Loading required package: preprocessCore >>> Welcome to oligo version 1.10.2 >>>> baseDir <- "/cchome/qichen2/Nimblegen_methylation/21863" >>>> (ndf <- list.files(baseDir, pattern = "ndf", full.names = TRUE)) >>> [1] >>> "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_ MeDIP_HX1. >>> ndf" >>>> (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1]) >>> [1] "/cchome/qichen2/Nimblegen_methylation/21863/38693602_532.xys" >>>> (pos <- list.files(baseDir, pattern = ".pos", full.names = TRUE)) >>> [1] >>> "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_ MeDIP_HX1. >>> pos" >>>> seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = xys,posFile = >>> pos, author = "AR", biocViews >>> = "AnnotationData", genomebuild = "HG 18", organism = "Human", species = >>> "Homo Sapiens") >>>> makePdInfoPackage(seed, destDir = "./") >>> ================================================================== ========== >>> ==== >>> Building annotation package for Nimblegen Tiling Array >>> NDF: ?081229_HG18_Promoter_MeDIP_HX1.ndf >>> POS: ?081229_HG18_Promoter_MeDIP_HX1.pos >>> XYS: ?38693602_532.xys >>> ================================================================== ========== >>> ==== >>> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.ndf ... OK >>> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.pos ... OK >>> Merging NDF and POS files... OK >>> Parsing file: 38693602_532.xys ... OK >>> Error in aggregate.data.frame(as.data.frame(x), ...) : >>> ?no rows to aggregate >>> Calls: makePdInfoPackage ... aggregate -> aggregate.default -> >>> aggregate.data.frame >>> In addition: Warning message: >>> In is.na(ndfdata[["SIGNAL"]]) : >>> ?is.na() applied to non-(list or vector) of type 'NULL' >>> Execution halted >>> >>> >>> >>> This email is intended only for the use of the individua...{{dropped:6}} >>> >>> _______________________________________________ >>> 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 >>> > > > > This email is intended only for the use of the individ...{{dropped:10}}
ADD REPLYlink written 9.7 years ago by Benilton Carvalho4.3k
Hi Benilton, Here is a sample of one of the xys files: >head 136413_532.xys # software=NimbleScan HD2-beta version=2.4.18 imagefile=./136413_532.tif designfile=/nfs/designs/Feinberg_HG18_Me_HX1.ndf designname=Feinberg_HG18_Me _HX1 designid=6353 date=Thu Oct 04 18:13:16 CDT 2007 border=0 ul_x=132.271 ul_y=67.752 ur_x=2992.461 ur_y=45.954 lr_x=3011.604 lr_ y=3865.026 ll_x=151.111 ll_y=3886.875 score=0.169 qcscore=0.377 locallyaligned=no correctAstig=no Knots= auto=no X Y SIGNAL COUNT 1 1 847.78 1 23 1 841.11 1 25 1 1180.67 1 27 1 727.33 1 29 1 427.33 1 31 1 460.00 1 33 1 561.67 1 35 1 638.00 1 37 1 2622.22 1 39 1 463.89 1 41 1 479.00 1 43 1 4508.89 1 45 1 4394.44 1 47 1 951.56 1 49 1 304.89 1 The rest of the xys files follow the same format, and do include NA where it should be. Thanks, Alex On 2/24/10 5:54 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: > Hi Alex, > > So, you're creating the XYS files yourself, right? > > These files should be sorted by X/Y coordinates and the SIGNAL columns > for the control probes should be NA. > > If you happen to have NimbleScan, it can create the XYS files directly > and appropriately. If you're going to create them manually, they > should follow the requirements above. Can you tell me if yours are > like this? > > THanks, > > b > > On Wed, Feb 24, 2010 at 6:01 PM, Alex Rodriguez > <arodrigu1 at="" bsd.uchicago.edu=""> wrote: >> Hi Benilton, >> Thanks for your prompt reply! >> The .xys file were created from .pair file which are from NimbleScan. >> >> Here is my output for sessionInfo(): >> >>> sessionInfo() >> R version 2.10.1 (2009-12-14) >> x86_64-unknown-linux-gnu >> >> 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=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? 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] pdInfoBuilder_1.10.1 oligo_1.10.2 ? ? ? ? preprocessCore_1.8.0 >> [4] oligoClasses_1.8.0 ? affxparser_1.18.0 ? ?RSQLite_0.8-2 >> [7] DBI_0.2-5 ? ? ? ? ? ?Biobase_2.6.1 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.14.0 ? ? ?Biostrings_2.14.12 IRanges_1.4.11 ? ? splines_2.10.1 >> >> Thanks for your input! >> >> Alex >> >> On 2/23/10 4:52 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: >> >>> Hi Alex, >>> >>> what's your sessionInfo()? >>> >>> Additionally, can you confirm you got the XYS files from NimbleGen or >>> NimbleScan? >>> >>> Thank you, >>> >>> benilton >>> >>> On Fri, Feb 19, 2010 at 7:44 PM, Alex Rodriguez >>> <arodrigu1 at="" bsd.uchicago.edu=""> wrote: >>>> Hi, >>>> I am new using pdInfoBuilder, so I may be missing something. I am trying to >>>> use pdInfoBuilder to make an annotation package. However, I get an error >>>> after the makePdInfoPackage(seed, destDir = "./") command. >>>> >>>> Error in aggregate.data.frame(as.data.frame(x), ...) : >>>> ?no rows to aggregate >>>> >>>> ?Has anybody encountered this message? >>>> >>>> Thanks!, >>>> >>>> Alex >>>> >>>> Here is my list of commands: >>>> >>>>> library(pdInfoBuilder) >>>> Loading required package: Biobase >>>> >>>> Welcome to Bioconductor >>>> >>>> ?Vignettes contain introductory material. To view, type >>>> ?'openVignette()'. To cite Bioconductor, see >>>> ?'citation("Biobase")' and for packages 'citation(pkgname)'. >>>> >>>> Loading required package: RSQLite >>>> Loading required package: DBI >>>> Loading required package: affxparser >>>> Loading required package: oligo >>>> Loading required package: oligoClasses >>>> Loading required package: preprocessCore >>>> Welcome to oligo version 1.10.2 >>>>> baseDir <- "/cchome/qichen2/Nimblegen_methylation/21863" >>>>> (ndf <- list.files(baseDir, pattern = "ndf", full.names = TRUE)) >>>> [1] >>>> "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_MeDI P_HX1>>>> . >>>> ndf" >>>>> (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1]) >>>> [1] "/cchome/qichen2/Nimblegen_methylation/21863/38693602_532.xys" >>>>> (pos <- list.files(baseDir, pattern = ".pos", full.names = TRUE)) >>>> [1] >>>> "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_MeDI P_HX1>>>> . >>>> pos" >>>>> seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = xys,posFile >>>>> = >>>> pos, author = "AR", biocViews >>>> = "AnnotationData", genomebuild = "HG 18", organism = "Human", species = >>>> "Homo Sapiens") >>>>> makePdInfoPackage(seed, destDir = "./") >>>> ====================================================================== =====>>>> = >>>> ==== >>>> Building annotation package for Nimblegen Tiling Array >>>> NDF: ?081229_HG18_Promoter_MeDIP_HX1.ndf >>>> POS: ?081229_HG18_Promoter_MeDIP_HX1.pos >>>> XYS: ?38693602_532.xys >>>> ====================================================================== =====>>>> = >>>> ==== >>>> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.ndf ... OK >>>> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.pos ... OK >>>> Merging NDF and POS files... OK >>>> Parsing file: 38693602_532.xys ... OK >>>> Error in aggregate.data.frame(as.data.frame(x), ...) : >>>> ?no rows to aggregate >>>> Calls: makePdInfoPackage ... aggregate -> aggregate.default -> >>>> aggregate.data.frame >>>> In addition: Warning message: >>>> In is.na(ndfdata[["SIGNAL"]]) : >>>> ?is.na() applied to non-(list or vector) of type 'NULL' >>>> Execution halted >>>> >>>> >>>> >>>> This email is intended only for the use of the individua...{{dropped:6}} >>>> >>>> _______________________________________________ >>>> 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 >>>> >> >> >> >> This email is intended only for the use of the individual or entity to which >> it is addressed and may contain information that is privileged and >> confidential. If the reader of this email message is not the intended >> recipient, you are hereby notified that any dissemination, distribution, or >> copying of this communication is prohibited. If you have received this email >> in error, please notify the sender and destroy/delete all copies of the >> transmittal. Thank you. >> >> This email is intended only for the use of the individua...{{dropped:8}}
ADD REPLYlink written 9.7 years ago by Alex Rodriguez40
Alex, much easier than that (because now I know what array you're working with) is to use the pre-made pd packages. They're going to make their way to BioC, but in the meantime use the instructions at: http://www.biostat.jhsph.edu/~maryee/charm/ b On Thu, Feb 25, 2010 at 4:59 PM, Alex Rodriguez <arodrigu1 at="" bsd.uchicago.edu=""> wrote: > Hi Benilton, > Here is a sample of one of the xys files: >>head 136413_532.xys > # software=NimbleScan HD2-beta ?version=2.4.18 ?imagefile=./136413_532.tif > designfile=/nfs/designs/Feinberg_HG18_Me_HX1.ndf > designname=Feinberg_HG18_Me > _HX1 ? ?designid=6353 ? date=Thu Oct 04 18:13:16 CDT 2007 ? ? ? border=0 > ul_x=132.271 ? ?ul_y=67.752 ? ? ur_x=2992.461 ? ur_y=45.954 > lr_x=3011.604 ? lr_ > y=3865.026 ? ? ?ll_x=151.111 ? ?ll_y=3886.875 ? score=0.169 > qcscore=0.377 ? locallyaligned=no ? ? ? correctAstig=no Knots= ?auto=no > X ? ? ? Y ? ? ? SIGNAL ?COUNT > 1 ? ? ? 1 ? ? ? 847.78 ?1 > 23 ? ? ?1 ? ? ? 841.11 ?1 > 25 ? ? ?1 ? ? ? 1180.67 1 > 27 ? ? ?1 ? ? ? 727.33 ?1 > 29 ? ? ?1 ? ? ? 427.33 ?1 > 31 ? ? ?1 ? ? ? 460.00 ?1 > 33 ? ? ?1 ? ? ? 561.67 ?1 > 35 ? ? ?1 ? ? ? 638.00 ?1 > 37 ? ? ?1 ? ? ? 2622.22 1 > 39 ? ? ?1 ? ? ? 463.89 ?1 > 41 ? ? ?1 ? ? ? 479.00 ?1 > 43 ? ? ?1 ? ? ? 4508.89 1 > 45 ? ? ?1 ? ? ? 4394.44 1 > 47 ? ? ?1 ? ? ? 951.56 ?1 > 49 ? ? ?1 ? ? ? 304.89 ?1 > > The rest of the xys files follow the same format, and do include NA where it > should be. > > Thanks, > > Alex > > > On 2/24/10 5:54 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: > >> Hi Alex, >> >> So, you're creating the XYS files yourself, right? >> >> These files should be sorted by X/Y coordinates and the SIGNAL columns >> for the control probes should be NA. >> >> If you happen to have NimbleScan, it can create the XYS files directly >> and appropriately. If you're going to create them manually, they >> should follow the requirements above. Can you tell me if yours are >> like this? >> >> THanks, >> >> b >> >> On Wed, Feb 24, 2010 at 6:01 PM, Alex Rodriguez >> <arodrigu1 at="" bsd.uchicago.edu=""> wrote: >>> Hi Benilton, >>> Thanks for your prompt reply! >>> The .xys file were created from .pair file which are from NimbleScan. >>> >>> Here is my output for sessionInfo(): >>> >>>> sessionInfo() >>> R version 2.10.1 (2009-12-14) >>> x86_64-unknown-linux-gnu >>> >>> 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=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >>> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? 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] pdInfoBuilder_1.10.1 oligo_1.10.2 ? ? ? ? preprocessCore_1.8.0 >>> [4] oligoClasses_1.8.0 ? affxparser_1.18.0 ? ?RSQLite_0.8-2 >>> [7] DBI_0.2-5 ? ? ? ? ? ?Biobase_2.6.1 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.14.0 ? ? ?Biostrings_2.14.12 IRanges_1.4.11 ? ? splines_2.10.1 >>> >>> Thanks for your input! >>> >>> Alex >>> >>> On 2/23/10 4:52 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: >>> >>>> Hi Alex, >>>> >>>> what's your sessionInfo()? >>>> >>>> Additionally, can you confirm you got the XYS files from NimbleGen or >>>> NimbleScan? >>>> >>>> Thank you, >>>> >>>> benilton >>>> >>>> On Fri, Feb 19, 2010 at 7:44 PM, Alex Rodriguez >>>> <arodrigu1 at="" bsd.uchicago.edu=""> wrote: >>>>> Hi, >>>>> I am new using pdInfoBuilder, so I may be missing something. I am trying to >>>>> use pdInfoBuilder to make an annotation package. However, I get an error >>>>> after the makePdInfoPackage(seed, destDir = "./") command. >>>>> >>>>> Error in aggregate.data.frame(as.data.frame(x), ...) : >>>>> ?no rows to aggregate >>>>> >>>>> ?Has anybody encountered this message? >>>>> >>>>> Thanks!, >>>>> >>>>> Alex >>>>> >>>>> Here is my list of commands: >>>>> >>>>>> library(pdInfoBuilder) >>>>> Loading required package: Biobase >>>>> >>>>> Welcome to Bioconductor >>>>> >>>>> ?Vignettes contain introductory material. To view, type >>>>> ?'openVignette()'. To cite Bioconductor, see >>>>> ?'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>> >>>>> Loading required package: RSQLite >>>>> Loading required package: DBI >>>>> Loading required package: affxparser >>>>> Loading required package: oligo >>>>> Loading required package: oligoClasses >>>>> Loading required package: preprocessCore >>>>> Welcome to oligo version 1.10.2 >>>>>> baseDir <- "/cchome/qichen2/Nimblegen_methylation/21863" >>>>>> (ndf <- list.files(baseDir, pattern = "ndf", full.names = TRUE)) >>>>> [1] >>>>> > "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_Me DIP_HX1>>>> > . >>>>> ndf" >>>>>> (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1]) >>>>> [1] "/cchome/qichen2/Nimblegen_methylation/21863/38693602_532.xys" >>>>>> (pos <- list.files(baseDir, pattern = ".pos", full.names = TRUE)) >>>>> [1] >>>>> > "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_Me DIP_HX1>>>> > . >>>>> pos" >>>>>> seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = xys,posFile >>>>>> = >>>>> pos, author = "AR", biocViews >>>>> = "AnnotationData", genomebuild = "HG 18", organism = "Human", species = >>>>> "Homo Sapiens") >>>>>> makePdInfoPackage(seed, destDir = "./") >>>>> > ==================================================================== =======>>>> > = >>>>> ==== >>>>> Building annotation package for Nimblegen Tiling Array >>>>> NDF: ?081229_HG18_Promoter_MeDIP_HX1.ndf >>>>> POS: ?081229_HG18_Promoter_MeDIP_HX1.pos >>>>> XYS: ?38693602_532.xys >>>>> > ==================================================================== =======>>>> > = >>>>> ==== >>>>> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.ndf ... OK >>>>> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.pos ... OK >>>>> Merging NDF and POS files... OK >>>>> Parsing file: 38693602_532.xys ... OK >>>>> Error in aggregate.data.frame(as.data.frame(x), ...) : >>>>> ?no rows to aggregate >>>>> Calls: makePdInfoPackage ... aggregate -> aggregate.default -> >>>>> aggregate.data.frame >>>>> In addition: Warning message: >>>>> In is.na(ndfdata[["SIGNAL"]]) : >>>>> ?is.na() applied to non-(list or vector) of type 'NULL' >>>>> Execution halted >>>>> >>>>> >>>>> >>>>> This email is intended only for the use of the individua...{{dropped:6}} >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>> >>> >>> >>> This email is intended only for the use of the individual or entity to which >>> it is addressed and may contain information that is privileged and >>> confidential. If the reader of this email message is not the intended >>> recipient, you are hereby notified that any dissemination, distribution, or >>> copying of this communication is prohibited. If you have received this email >>> in error, please notify the sender and destroy/delete all copies of the >>> transmittal. Thank you. >>> >>> > > > > This email is intended only for the use of the individ...{{dropped:10}}
ADD REPLYlink written 9.7 years ago by Benilton Carvalho4.3k
Hi Benilton, Sorry, I copied the wrong segment of xys files. Here is the header of the actual xys file which is different than the pre-made package, I think. >head 41779702_635.xys # software=NimbleScan version=2.5.28 imagefile=/nfs/bioinfo/production/analysis/active/21863y/41779702_635. tif designfile=/nfs/designs/081229_HG18_Promote r_MeDIP_HX1.ndf designname=081229_HG18_Promoter_MeDIP_HX1 designid=8567 date=Mon Dec 21 10:23:20 CST 2009 border=0 ul_x=4.500 ul_y=3.500ur_x=1050.500 ur_y=3.500 lr_x=1050.500 lr_y=1399.500 ll_x=4.500 ll_y=1399.500 score=0.000 qcscore=0.233 locallyaligned=no correctAsti g=no Knots= auto=no X Y Signal Count 259 1 440.00 1 465 1 468.00 1 725 1 377.00 1 797 1 453.00 1 827 1 303.00 1 859 1 399.00 1 234 2 560.00 1 440 2 2471.00 1 464 2 393.00 1 722 2 1470.00 1 730 2 300.00 1 1028 2 333.00 1 189 3 336.00 1 257 3 392.00 1 379 3 423.00 1 437 3 299.00 1 701 3 337.00 1 811 3 522.00 1 190 4 497.00 1 334 4 362.00 1 Does this look correct? Thanks and sorry for the confusion, Alex On 2/25/10 12:57 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: > Alex, > > much easier than that (because now I know what array you're working > with) is to use the pre-made pd packages. They're going to make their > way to BioC, but in the meantime use the instructions at: > > http://www.biostat.jhsph.edu/~maryee/charm/ > > b > > On Thu, Feb 25, 2010 at 4:59 PM, Alex Rodriguez > <arodrigu1 at="" bsd.uchicago.edu=""> wrote: >> Hi Benilton, >> Here is a sample of one of the xys files: >>> head 136413_532.xys >> # software=NimbleScan HD2-beta ?version=2.4.18 ?imagefile=./136413_532.tif >> designfile=/nfs/designs/Feinberg_HG18_Me_HX1.ndf >> designname=Feinberg_HG18_Me >> _HX1 ? ?designid=6353 ? date=Thu Oct 04 18:13:16 CDT 2007 ? ? ? border=0 >> ul_x=132.271 ? ?ul_y=67.752 ? ? ur_x=2992.461 ? ur_y=45.954 >> lr_x=3011.604 ? lr_ >> y=3865.026 ? ? ?ll_x=151.111 ? ?ll_y=3886.875 ? score=0.169 >> qcscore=0.377 ? locallyaligned=no ? ? ? correctAstig=no Knots= ?auto=no >> X ? ? ? Y ? ? ? SIGNAL ?COUNT >> 1 ? ? ? 1 ? ? ? 847.78 ?1 >> 23 ? ? ?1 ? ? ? 841.11 ?1 >> 25 ? ? ?1 ? ? ? 1180.67 1 >> 27 ? ? ?1 ? ? ? 727.33 ?1 >> 29 ? ? ?1 ? ? ? 427.33 ?1 >> 31 ? ? ?1 ? ? ? 460.00 ?1 >> 33 ? ? ?1 ? ? ? 561.67 ?1 >> 35 ? ? ?1 ? ? ? 638.00 ?1 >> 37 ? ? ?1 ? ? ? 2622.22 1 >> 39 ? ? ?1 ? ? ? 463.89 ?1 >> 41 ? ? ?1 ? ? ? 479.00 ?1 >> 43 ? ? ?1 ? ? ? 4508.89 1 >> 45 ? ? ?1 ? ? ? 4394.44 1 >> 47 ? ? ?1 ? ? ? 951.56 ?1 >> 49 ? ? ?1 ? ? ? 304.89 ?1 >> >> The rest of the xys files follow the same format, and do include NA where it >> should be. >> >> Thanks, >> >> Alex >> >> >> On 2/24/10 5:54 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: >> >>> Hi Alex, >>> >>> So, you're creating the XYS files yourself, right? >>> >>> These files should be sorted by X/Y coordinates and the SIGNAL columns >>> for the control probes should be NA. >>> >>> If you happen to have NimbleScan, it can create the XYS files directly >>> and appropriately. If you're going to create them manually, they >>> should follow the requirements above. Can you tell me if yours are >>> like this? >>> >>> THanks, >>> >>> b >>> >>> On Wed, Feb 24, 2010 at 6:01 PM, Alex Rodriguez >>> <arodrigu1 at="" bsd.uchicago.edu=""> wrote: >>>> Hi Benilton, >>>> Thanks for your prompt reply! >>>> The .xys file were created from .pair file which are from NimbleScan. >>>> >>>> Here is my output for sessionInfo(): >>>> >>>>> sessionInfo() >>>> R version 2.10.1 (2009-12-14) >>>> x86_64-unknown-linux-gnu >>>> >>>> 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=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >>>> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? 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] pdInfoBuilder_1.10.1 oligo_1.10.2 ? ? ? ? preprocessCore_1.8.0 >>>> [4] oligoClasses_1.8.0 ? affxparser_1.18.0 ? ?RSQLite_0.8-2 >>>> [7] DBI_0.2-5 ? ? ? ? ? ?Biobase_2.6.1 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] affyio_1.14.0 ? ? ?Biostrings_2.14.12 IRanges_1.4.11 ? ? splines_2.10.1 >>>> >>>> Thanks for your input! >>>> >>>> Alex >>>> >>>> On 2/23/10 4:52 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: >>>> >>>>> Hi Alex, >>>>> >>>>> what's your sessionInfo()? >>>>> >>>>> Additionally, can you confirm you got the XYS files from NimbleGen or >>>>> NimbleScan? >>>>> >>>>> Thank you, >>>>> >>>>> benilton >>>>> >>>>> On Fri, Feb 19, 2010 at 7:44 PM, Alex Rodriguez >>>>> <arodrigu1 at="" bsd.uchicago.edu=""> wrote: >>>>>> Hi, >>>>>> I am new using pdInfoBuilder, so I may be missing something. I am trying >>>>>> to >>>>>> use pdInfoBuilder to make an annotation package. However, I get an error >>>>>> after the makePdInfoPackage(seed, destDir = "./") command. >>>>>> >>>>>> Error in aggregate.data.frame(as.data.frame(x), ...) : >>>>>> ?no rows to aggregate >>>>>> >>>>>> ?Has anybody encountered this message? >>>>>> >>>>>> Thanks!, >>>>>> >>>>>> Alex >>>>>> >>>>>> Here is my list of commands: >>>>>> >>>>>>> library(pdInfoBuilder) >>>>>> Loading required package: Biobase >>>>>> >>>>>> Welcome to Bioconductor >>>>>> >>>>>> ?Vignettes contain introductory material. To view, type >>>>>> ?'openVignette()'. To cite Bioconductor, see >>>>>> ?'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>>> >>>>>> Loading required package: RSQLite >>>>>> Loading required package: DBI >>>>>> Loading required package: affxparser >>>>>> Loading required package: oligo >>>>>> Loading required package: oligoClasses >>>>>> Loading required package: preprocessCore >>>>>> Welcome to oligo version 1.10.2 >>>>>>> baseDir <- "/cchome/qichen2/Nimblegen_methylation/21863" >>>>>>> (ndf <- list.files(baseDir, pattern = "ndf", full.names = TRUE)) >>>>>> [1] >>>>>> >> "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_M eDIP_HX1>> >> >> >> . >>>>>> ndf" >>>>>>> (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1]) >>>>>> [1] "/cchome/qichen2/Nimblegen_methylation/21863/38693602_532.xys" >>>>>>> (pos <- list.files(baseDir, pattern = ".pos", full.names = TRUE)) >>>>>> [1] >>>>>> >> "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_M eDIP_HX1>> >> >> >> . >>>>>> pos" >>>>>>> seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = >>>>>>> xys,posFile >>>>>>> = >>>>>> pos, author = "AR", biocViews >>>>>> = "AnnotationData", genomebuild = "HG 18", organism = "Human", species = >>>>>> "Homo Sapiens") >>>>>>> makePdInfoPackage(seed, destDir = "./") >>>>>> >> =================================================================== ========>> >> >> >> = >>>>>> ==== >>>>>> Building annotation package for Nimblegen Tiling Array >>>>>> NDF: ?081229_HG18_Promoter_MeDIP_HX1.ndf >>>>>> POS: ?081229_HG18_Promoter_MeDIP_HX1.pos >>>>>> XYS: ?38693602_532.xys >>>>>> >> =================================================================== ========>> >> >> >> = >>>>>> ==== >>>>>> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.ndf ... OK >>>>>> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.pos ... OK >>>>>> Merging NDF and POS files... OK >>>>>> Parsing file: 38693602_532.xys ... OK >>>>>> Error in aggregate.data.frame(as.data.frame(x), ...) : >>>>>> ?no rows to aggregate >>>>>> Calls: makePdInfoPackage ... aggregate -> aggregate.default -> >>>>>> aggregate.data.frame >>>>>> In addition: Warning message: >>>>>> In is.na(ndfdata[["SIGNAL"]]) : >>>>>> ?is.na() applied to non-(list or vector) of type 'NULL' >>>>>> Execution halted >>>>>> >>>>>> >>>>>> >>>>>> This email is intended only for the use of the individua...{{dropped:6}} >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>>> >>>> >>>> >>>> >>>> This email is intended only for the use of the individual or entity to >>>> which >>>> it is addressed and may contain information that is privileged and >>>> confidential. If the reader of this email message is not the intended >>>> recipient, you are hereby notified that any dissemination, distribution, or >>>> copying of this communication is prohibited. If you have received this >>>> email >>>> in error, please notify the sender and destroy/delete all copies of the >>>> transmittal. Thank you. >>>> >>>> >> >> >> >> This email is intended only for the use of the individual or entity to which >> it is addressed and may contain information that is privileged and >> confidential. If the reader of this email message is not the intended >> recipient, you are hereby notified that any dissemination, distribution, or >> copying of this communication is prohibited. If you have received this email >> in error, please notify the sender and destroy/delete all copies of the >> transmittal. Thank you. >> >> This email is intended only for the use of the individua...{{dropped:8}}
ADD REPLYlink written 9.7 years ago by Alex Rodriguez40
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