ChIPpeakAnno
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@brian-james-gadd-5126
Last seen 7.7 years ago
I am relatively new to R and am trying to use ChIPpeakAnno. I am having some difficulty getting the ChIPpeakAnno library to load correctly. The annotatePeakInBatch function still runs but fails to properly annotate genes on the minus strand. Specifically, upon loading the ChIPpeakAnno library a variety of objects are masked from several attached packages as detailed in the printout below. The sessionInfo() print out is below as well. Any advice on how to ensure everything loads correctly would be greatly appreciated; I haven't been able to find anything after scouring bioconductor, CRAN, or Google and I'm at a loss. Thanks! > library(ChIPpeakAnno) Loading required package: biomaRt Loading required package: multtest Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: IRanges Attaching package: ?IRanges? The following object(s) are masked from ?package:Biobase?: updateObject The following object(s) are masked from ?package:base?: cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union Loading required package: Biostrings Loading required package: BSgenome Loading required package: GenomicRanges Loading required package: BSgenome.Ecoli.NCBI.20080805 Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: org.Hs.eg.db Loading required package: limma Loading required package: gplots Loading required package: gtools Loading required package: gdata gdata: Unable to locate valid perl interpreter gdata: gdata: read.xls() will be unable to read Excel XLS and XLSX files unless the 'perl=' argument is used to specify the location of a valid perl gdata: intrpreter. gdata: gdata: (To avoid display of this message in the future, please ensure perl is installed and available on the executable search path.) gdata: Unable to load perl libaries needed by read.xls() gdata: to support 'XLX' (Excel 97-2004) files. gdata: Unable to load perl libaries needed by read.xls() gdata: to support 'XLSX' (Excel 2007+) files. gdata: Run the function 'installXLSXsupport()' gdata: to automatically download and install the perl gdata: libaries needed to support Excel XLS and XLSX formats. Attaching package: ?gdata? The following object(s) are masked from ?package:IRanges?: trim The following object(s) are masked from ?package:Biobase?: combine The following object(s) are masked from ?package:stats?: nobs The following object(s) are masked from ?package:utils?: object.size Loading required package: caTools Loading required package: bitops Attaching package: ?caTools? The following object(s) are masked from ?package:IRanges?: runmean Loading required package: grid Loading required package: KernSmooth KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Attaching package: ?gplots? The following object(s) are masked from ?package:IRanges?: space The following object(s) are masked from ?package:multtest?: wapply The following object(s) are masked from ?package:stats?: lowess Warning message: replacing previous import ?space? when loading ?IRanges? > > sessionInfo() R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] ChIPpeakAnno_2.2.0 gplots_2.10.1 KernSmooth_2.23-7 caTools_1.12 [5] bitops_1.0-4.1 gdata_2.8.2 gtools_2.6.2 limma_3.10.2 [9] org.Hs.eg.db_2.6.4 GO.db_2.6.1 RSQLite_0.11.1 DBI_0.2-5 [13] AnnotationDbi_1.16.16 BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.22.0 GenomicRanges_1.6.7 [17] Biostrings_2.22.0 IRanges_1.12.6 multtest_2.10.0 Biobase_2.14.0 [21] biomaRt_2.10.0 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] MASS_7.3-17 RCurl_1.91-1.1 splines_2.14.1 survival_2.36-12 tools_2.14.1 XML_3.9-4.1 I attempted this after getting R and bioconductor up and running first: Fresh Install of R 2.14.1 in Windows 7. Assigned write permission to the library folder to allow package installation. source("http://bioconductor.org/biocLite.R") biocLite() biocLite(c("ChIPpeakAnno")) update.packages(repos=biocinstallRepos(), ask=FALSE) ---- Brian Gadd PhD Candidate Cell, Molecular and Developmental Biology University of California Riverside Tel: 19513130505 Email: bgadd001 at student.ucr.edu
GO BSgenome annotate BSgenome ChIPpeakAnno GO BSgenome annotate BSgenome ChIPpeakAnno • 1.2k views
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Brian Gadd ▴ 10
@brian-gadd-5127
Last seen 7.7 years ago
I am relatively new to R and am trying to use ChIPpeakAnno. ?I am having some difficulty getting the ChIPpeakAnno library to load correctly. The annotatePeakInBatch function still runs but fails to properly annotate genes on the minus strand. Specifically, upon loading the ChIPpeakAnno library a variety of objects are masked from several attached packages as detailed in the printout below. The sessionInfo() print out is below as well. Any advice on how to ensure everything loads correctly would be greatly appreciated; I haven't been able to find anything after scouring bioconductor, CRAN, or Google and I'm at a loss. Thanks! > library(ChIPpeakAnno) Loading required package: biomaRt Loading required package: multtest Loading required package: Biobase Welcome to Bioconductor ? Vignettes contain introductory material. To view, type ? 'browseVignettes()'. To cite Bioconductor, see ? 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: IRanges Attaching package: ?IRanges? The following object(s) are masked from ?package:Biobase?: ? ? updateObject The following object(s) are masked from ?package:base?: ? ? cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union Loading required package: Biostrings Loading required package: BSgenome Loading required package: GenomicRanges Loading required package: BSgenome.Ecoli.NCBI.20080805 Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: org.Hs.eg.db Loading required package: limma Loading required package: gplots Loading required package: gtools Loading required package: gdata gdata: Unable to locate valid perl interpreter gdata: gdata: read.xls() will be unable to read Excel XLS and XLSX files unless the 'perl=' argument is used to specify the location of a valid perl gdata: intrpreter. gdata: gdata: (To avoid display of this message in the future, please ensure perl is installed and available on the executable search path.) gdata: Unable to load perl libaries needed by read.xls() gdata: to support 'XLX' (Excel 97-2004) files. gdata: Unable to load perl libaries needed by read.xls() gdata: to support 'XLSX' (Excel 2007+) files. gdata: Run the function 'installXLSXsupport()' gdata: to automatically download and install the perl gdata: libaries needed to support Excel XLS and XLSX formats. Attaching package: ?gdata? The following object(s) are masked from ?package:IRanges?: ? ? trim The following object(s) are masked from ?package:Biobase?: ? ? combine The following object(s) are masked from ?package:stats?: ? ? nobs The following object(s) are masked from ?package:utils?: ? ? object.size Loading required package: caTools Loading required package: bitops Attaching package: ?caTools? The following object(s) are masked from ?package:IRanges?: ? ? runmean Loading required package: grid Loading required package: KernSmooth KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Attaching package: ?gplots? The following object(s) are masked from ?package:IRanges?: ? ? space The following object(s) are masked from ?package:multtest?: ? ? wapply The following object(s) are masked from ?package:stats?: ? ? lowess Warning message: replacing previous import ?space? when loading ?IRanges? > > sessionInfo() R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United States.1252 ? ?LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets methods ? base other attached packages: ?[1] ChIPpeakAnno_2.2.0 ? ? ? ? ? ? ? ? ?gplots_2.10.1 ? ? ? KernSmooth_2.23-7 ? ? ? ? ? ? ? ? ? caTools_1.12 ?[5] bitops_1.0-4.1 ? ? ? ? ? ? ? ? ? ? ?gdata_2.8.2 ? ? ? gtools_2.6.2 ? ? ? ? ? ? ? ? ? ? ? ?limma_3.10.2 ?[9] org.Hs.eg.db_2.6.4 ? ? ? ? ? ? ? ? ?GO.db_2.6.1 ? ? ? RSQLite_0.11.1 ? ? ? ? ? ? ? ? ? ? ?DBI_0.2-5 [13] AnnotationDbi_1.16.16 BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.22.0 GenomicRanges_1.6.7 [17] Biostrings_2.22.0 ? ? ? ? ? ? ? ? ? IRanges_1.12.6 ? ? ?multtest_2.10.0 ? ? ? ? ? ? ? ? ? ? Biobase_2.14.0 [21] biomaRt_2.10.0 ? ? ? ? ? ? ? ? ? ? ?BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] MASS_7.3-17 ? ? ?RCurl_1.91-1.1 ? splines_2.14.1 survival_2.36-12 tools_2.14.1 ? ? XML_3.9-4.1 I attempted this after getting R and bioconductor up and running first: Fresh Install of R 2.14.1 in Windows 7. Assigned write permission to the library folder to allow package installation. source("http://bioconductor.org/biocLite.R") biocLite() biocLite(c("ChIPpeakAnno")) update.packages(repos=biocinstallRepos(), ask=FALSE) ---- Brian Gadd PhD Candidate Cell, Molecular and Developmental Biology University of California Riverside Tel:?19513130505 Email:?bgadd001 at ucr.edu
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On Sat, Feb 18, 2012 at 11:11 PM, Brian Gadd <bgadd001 at="" ucr.edu=""> wrote: > I am relatively new to R and am trying to use ChIPpeakAnno. ?I am > having some difficulty getting the ChIPpeakAnno library to load > correctly. The annotatePeakInBatch function still runs but fails to > properly annotate genes on the minus strand. > > Specifically, upon loading the ChIPpeakAnno library a variety of > objects are masked from several attached packages as detailed in the > printout below. ?The sessionInfo() print out is below as well. Hi, Brian. These messages are informational and will likely not affect everyday use. I suggest you ignore them for now. You mention something about chipPeakAnno working but not annotating on the minus strand. If you still have questions on that front, perhaps another email relating those issues is warranted. Sean > Any advice on how to ensure everything loads correctly would be > greatly appreciated; I haven't been able to find anything after > scouring bioconductor, CRAN, or Google and I'm at a loss. ?Thanks! > >> library(ChIPpeakAnno) > Loading required package: biomaRt > Loading required package: multtest > Loading required package: Biobase > > Welcome to Bioconductor > > ? Vignettes contain introductory material. To view, type > ? 'browseVignettes()'. To cite Bioconductor, see > ? 'citation("Biobase")' and for packages 'citation("pkgname")'. > > Loading required package: IRanges > > Attaching package: ?IRanges? > > The following object(s) are masked from ?package:Biobase?: > > ? ? updateObject > > The following object(s) are masked from ?package:base?: > > ? ? cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, > pmin, pmin.int, rbind, rep.int, setdiff, table, union > > Loading required package: Biostrings > Loading required package: BSgenome > Loading required package: GenomicRanges > Loading required package: BSgenome.Ecoli.NCBI.20080805 > Loading required package: GO.db > Loading required package: AnnotationDbi > Loading required package: DBI > > Loading required package: org.Hs.eg.db > > Loading required package: limma > Loading required package: gplots > Loading required package: gtools > Loading required package: gdata > gdata: Unable to locate valid perl interpreter > gdata: > gdata: read.xls() will be unable to read Excel XLS and XLSX files > unless the 'perl=' argument is used to specify the location of a valid > perl > gdata: intrpreter. > gdata: > gdata: (To avoid display of this message in the future, please ensure > perl is installed and available on the executable search path.) > gdata: Unable to load perl libaries needed by read.xls() > gdata: to support 'XLX' (Excel 97-2004) files. > > gdata: Unable to load perl libaries needed by read.xls() > gdata: to support 'XLSX' (Excel 2007+) files. > > gdata: Run the function 'installXLSXsupport()' > gdata: to automatically download and install the perl > gdata: libaries needed to support Excel XLS and XLSX formats. > > Attaching package: ?gdata? > > The following object(s) are masked from ?package:IRanges?: > > ? ? trim > > The following object(s) are masked from ?package:Biobase?: > > ? ? combine > > The following object(s) are masked from ?package:stats?: > > ? ? nobs > > The following object(s) are masked from ?package:utils?: > > ? ? object.size > > Loading required package: caTools > Loading required package: bitops > > Attaching package: ?caTools? > > The following object(s) are masked from ?package:IRanges?: > > ? ? runmean > > Loading required package: grid > Loading required package: KernSmooth > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > > Attaching package: ?gplots? > > The following object(s) are masked from ?package:IRanges?: > > ? ? space > > The following object(s) are masked from ?package:multtest?: > > ? ? wapply > > The following object(s) are masked from ?package:stats?: > > ? ? lowess > > Warning message: > replacing previous import ?space? when loading ?IRanges? >> > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United > States.1252 ? ?LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets > methods ? base > > other attached packages: > ?[1] ChIPpeakAnno_2.2.0 ? ? ? ? ? ? ? ? ?gplots_2.10.1 > ? ? ? KernSmooth_2.23-7 ? ? ? ? ? ? ? ? ? caTools_1.12 > ?[5] bitops_1.0-4.1 ? ? ? ? ? ? ? ? ? ? ?gdata_2.8.2 > ? ? ? gtools_2.6.2 ? ? ? ? ? ? ? ? ? ? ? ?limma_3.10.2 > ?[9] org.Hs.eg.db_2.6.4 ? ? ? ? ? ? ? ? ?GO.db_2.6.1 > ? ? ? RSQLite_0.11.1 ? ? ? ? ? ? ? ? ? ? ?DBI_0.2-5 > [13] AnnotationDbi_1.16.16 > BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.22.0 > ?GenomicRanges_1.6.7 > [17] Biostrings_2.22.0 ? ? ? ? ? ? ? ? ? IRanges_1.12.6 > ?? ? ?multtest_2.10.0 ? ? ? ? ? ? ? ? ? ? Biobase_2.14.0 > [21] biomaRt_2.10.0 ? ? ? ? ? ? ? ? ? ? ?BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] MASS_7.3-17 ? ? ?RCurl_1.91-1.1 ? splines_2.14.1 > survival_2.36-12 tools_2.14.1 ? ? XML_3.9-4.1 > > > > I attempted this after getting R and bioconductor up and running first: > Fresh Install of R 2.14.1 in Windows 7. > Assigned write permission to the library folder to allow package installation. > source("http://bioconductor.org/biocLite.R") > biocLite() > biocLite(c("ChIPpeakAnno")) > update.packages(repos=biocinstallRepos(), ask=FALSE) > > > ---- > Brian Gadd > PhD Candidate > Cell, Molecular and Developmental Biology > University of California Riverside > > Tel:?19513130505 > Email:?bgadd001 at ucr.edu > > _______________________________________________ > 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
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