results.summary function returns error
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Hello everybody out there using the simpleaffy Bioconductor package, In order to get started with microarray analysis, I'm trying to reproduce the steps in the Vignette of the simpleaffy package. I downloaded the sample CEL files from the homepage of the bioinformatics group of the university of Manchester (http://bioinformatics.picr.man.ac.uk/experiments/amplification/CEL/) and performed the following steps: R> library(simpleaffy) R> x <- read.affy("covdesc") R> x.rma <- call.exprs(x,"rma") R> pw <- pairwise.comparison(x.rma,"rna",c("10ng","100ng")) R> pw.filtered <- pairwise.filter(pw) R> library("hgu133a.db") So far, so good. The following command yields the error message: R> summary <- results.summary(pw.filtered,"hgu133a.db") Error is get(paste(cdfname, "SYMBOL", sep = "")) : Object "hgu133a.dbSymbol" not found I've done extensive web search and found out there's been a migration of the annotation data to SQLite format. This seems to cause problems concerning the annotation carried out by the "results.summary" function. In the thread https://stat.ethz.ch/pipermail/bioconductor/2009-January/025787.html is mentioning a very similar problem I have and solves this thread by redefining the "get.annotation" function get.annotation <- function (x, cdfname, verbose = FALSE) { library(cdfname, character.only = TRUE) cdfname <- sub("\\.db$", "", cdfname) ## add this line } I tried this to no success. Moreover, I entered the following commands, but also got errors: R> summary <- results.summary(pw.filtered,hgu133a.db) R> summary <- results.summary(pw.filtered,"hgu133a") R> summary <- results.summary(pw.filtered,hgu133a) What additional diagnostics could I run to pin down the problem? Kind regards, Julia -- output of sessionInfo(): R version 2.14.1 (2011-12-22) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133a.db_2.6.3 org.Hs.eg.db_2.6.4 RSQLite_0.11.2 [4] DBI_0.2-5 hgu133acdf_2.9.1 AnnotationDbi_1.16.19 [7] simpleaffy_2.30.0 gcrma_2.26.0 genefilter_1.36.0 [10] affy_1.32.1 Biobase_2.14.0 loaded via a namespace (and not attached): [1] affyio_1.22.0 annotate_1.32.3 BiocInstaller_1.2.1 [4] Biostrings_2.22.0 IRanges_1.12.6 preprocessCore_1.16.0 [7] splines_2.14.1 survival_2.36-10 tools_2.14.1 [10] xtable_1.7-0 zlibbioc_1.0.1 -- Sent via the guest posting facility at bioconductor.org.
Microarray Annotation hgu133a simpleaffy Microarray Annotation hgu133a simpleaffy • 917 views
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@steve-lianoglou-2771
Last seen 1 hour ago
Denali
Hi Julia, You are using a rather outdated version of R and Bioconductor at this point. I'd suggest you upgrade to the latest version of R (2.15.2) and reinstall the relevant bioconductor packages via: R> source("http://bioconductor.org/biocLite.R") R> biocLite(c('your', 'packages', 'of', 'interest')) I'm not too familiar w/ the workings of the simpleaffy package, so can't really comment on your code, per se, but you'll need current versions of the packages you're using to get the best help (these problems might even disappear on their own). -steve On Fri, Nov 16, 2012 at 4:49 AM, Julia Jacobson [guest] <guest at="" bioconductor.org=""> wrote: > > Hello everybody out there using the simpleaffy Bioconductor package, > > In order to get started with microarray analysis, I'm trying to reproduce the steps in the Vignette of the simpleaffy package. > I downloaded the sample CEL files from the homepage of the bioinformatics group of the university of Manchester (http://bioinformatics.picr.man.ac.uk/experiments/amplification/CEL/) and performed the following steps: > > R> library(simpleaffy) > R> x <- read.affy("covdesc") > R> x.rma <- call.exprs(x,"rma") > R> pw <- pairwise.comparison(x.rma,"rna",c("10ng","100ng")) > R> pw.filtered <- pairwise.filter(pw) > R> library("hgu133a.db") > > So far, so good. The following command yields the error message: > > R> summary <- results.summary(pw.filtered,"hgu133a.db") > Error is get(paste(cdfname, "SYMBOL", sep = "")) : > Object "hgu133a.dbSymbol" not found > > I've done extensive web search and found out there's been a migration of the annotation data to SQLite format. This seems to cause problems concerning the annotation carried out by the "results.summary" function. > In the thread https://stat.ethz.ch/pipermail/bioconductor/2009-January/025787.html is mentioning a very similar problem I have and solves this thread by redefining the "get.annotation" function > > get.annotation <- function (x, cdfname, verbose = FALSE) { > library(cdfname, character.only = TRUE) > cdfname <- sub("\\.db$", "", cdfname) ## add this line > } > > I tried this to no success. > Moreover, I entered the following commands, but also got errors: > > > R> summary <- results.summary(pw.filtered,hgu133a.db) > R> summary <- results.summary(pw.filtered,"hgu133a") > R> summary <- results.summary(pw.filtered,hgu133a) > > What additional diagnostics could I run to pin down the problem? > > Kind regards, > Julia > > -- output of sessionInfo(): > > R version 2.14.1 (2011-12-22) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133a.db_2.6.3 org.Hs.eg.db_2.6.4 RSQLite_0.11.2 > [4] DBI_0.2-5 hgu133acdf_2.9.1 AnnotationDbi_1.16.19 > [7] simpleaffy_2.30.0 gcrma_2.26.0 genefilter_1.36.0 > [10] affy_1.32.1 Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] affyio_1.22.0 annotate_1.32.3 BiocInstaller_1.2.1 > [4] Biostrings_2.22.0 IRanges_1.12.6 preprocessCore_1.16.0 > [7] splines_2.14.1 survival_2.36-10 tools_2.14.1 > [10] xtable_1.7-0 zlibbioc_1.0.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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@james-w-macdonald-5106
Last seen 4 hours ago
United States
Hi Julia, On 11/16/2012 4:49 AM, Julia Jacobson [guest] wrote: > Hello everybody out there using the simpleaffy Bioconductor package, > > In order to get started with microarray analysis, I'm trying to reproduce the steps in the Vignette of the simpleaffy package. > I downloaded the sample CEL files from the homepage of the bioinformatics group of the university of Manchester (http://bioinformatics.picr.man.ac.uk/experiments/amplification/CEL/) and performed the following steps: > > R> library(simpleaffy) > R> x<- read.affy("covdesc") > R> x.rma<- call.exprs(x,"rma") > R> pw<- pairwise.comparison(x.rma,"rna",c("10ng","100ng")) > R> pw.filtered<- pairwise.filter(pw) > R> library("hgu133a.db") > > So far, so good. The following command yields the error message: > > R> summary<- results.summary(pw.filtered,"hgu133a.db") But this isn't the same thing as what is in the vignette: summary <- results.summary(pw.filtered,"hgu133a") Note that there isn't a .db extension. > Error is get(paste(cdfname, "SYMBOL", sep = "")) : > Object "hgu133a.dbSymbol" not found Hence the error. Even though the annotation packages now use a SQLite backend, the 'regular' get() and mget() functions still work. But the environment argument is still hgu133aSYMBOL, not the hgu133a.dbSYMBOL that ends up being used in your case. Best, Jim > > I've done extensive web search and found out there's been a migration of the annotation data to SQLite format. This seems to cause problems concerning the annotation carried out by the "results.summary" function. > In the thread https://stat.ethz.ch/pipermail/bioconductor/2009-January/025787.html is mentioning a very similar problem I have and solves this thread by redefining the "get.annotation" function > > get.annotation<- function (x, cdfname, verbose = FALSE) { > library(cdfname, character.only = TRUE) > cdfname<- sub("\\.db$", "", cdfname) ## add this line > } > > I tried this to no success. > Moreover, I entered the following commands, but also got errors: > > > R> summary<- results.summary(pw.filtered,hgu133a.db) > R> summary<- results.summary(pw.filtered,"hgu133a") > R> summary<- results.summary(pw.filtered,hgu133a) > > What additional diagnostics could I run to pin down the problem? > > Kind regards, > Julia > > -- output of sessionInfo(): > > R version 2.14.1 (2011-12-22) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hgu133a.db_2.6.3 org.Hs.eg.db_2.6.4 RSQLite_0.11.2 > [4] DBI_0.2-5 hgu133acdf_2.9.1 AnnotationDbi_1.16.19 > [7] simpleaffy_2.30.0 gcrma_2.26.0 genefilter_1.36.0 > [10] affy_1.32.1 Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] affyio_1.22.0 annotate_1.32.3 BiocInstaller_1.2.1 > [4] Biostrings_2.22.0 IRanges_1.12.6 preprocessCore_1.16.0 > [7] splines_2.14.1 survival_2.36-10 tools_2.14.1 > [10] xtable_1.7-0 zlibbioc_1.0.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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
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