Problem using justGCRMA
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@antonio-mendes-4625
Last seen 7.1 years ago
Hi I'm trying to use justgcrma to normalize data from affy Plasmodium/anopheles genome array and am getting the error copied bellow. I'm running version 2.13.0 of R and version 2.8.1 of gcrma. Can anybody help how to overcome this? thanks Antonio > library(gcrma) Loading required package: affy 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")'. > setwd("H:\\MozzyData") > normalized<-justGCRMA() Computing affinitiesLoading required package: AnnotationDbi [1] "Checking to see if your internet connection works..." trying URL ' http://bioconductor.org/packages/2.8/data/annotation/bin/windows/contr ib/2.13/plasmodiumanophelesprobe_2.8.0.zip ' Content type 'application/zip' length 3553447 bytes (3.4 Mb) opened URL downloaded 3.4 Mb package 'plasmodiumanophelesprobe' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Users\Antonio\AppData\Local\Temp\RtmpiYHe0U\downloaded_packages Loading required package: AnnotationDbi Error in loadNamespace(i, c(lib.loc, .libPaths())) : there is no package called 'DBI' Error: package 'AnnotationDbi' could not be loaded [[alternative HTML version deleted]]
gcrma gcrma • 775 views
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@james-w-macdonald-5106
Last seen 12 hours ago
United States
Hi Antonio, On 5/5/2011 4:57 AM, Antonio Mendes wrote: > Hi > I'm trying to use justgcrma to normalize data from affy Plasmodium/anopheles > genome array and am getting the error copied bellow. I'm running version > 2.13.0 of R and version 2.8.1 of gcrma. Can anybody help how to overcome > this? > > thanks > Antonio > > >> library(gcrma) > Loading required package: affy > 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")'. > >> setwd("H:\\MozzyData") >> normalized<-justGCRMA() > Computing affinitiesLoading required package: AnnotationDbi > [1] "Checking to see if your internet connection works..." > trying URL ' > http://bioconductor.org/packages/2.8/data/annotation/bin/windows/con trib/2.13/plasmodiumanophelesprobe_2.8.0.zip > ' > Content type 'application/zip' length 3553447 bytes (3.4 Mb) > opened URL > downloaded 3.4 Mb > > package 'plasmodiumanophelesprobe' successfully unpacked and MD5 sums > checked > > The downloaded packages are in > C:\Users\Antonio\AppData\Local\Temp\RtmpiYHe0U\downloaded_packages > Loading required package: AnnotationDbi > Error in loadNamespace(i, c(lib.loc, .libPaths())) : > there is no package called 'DBI' > Error: package 'AnnotationDbi' could not be loaded Looks like you don't have DBI installed. How did you install AnnotationDbi? You should always remember to give us the output of sessionInfo() so we can see if you have mismatched packages. The easiest fix will be source("http://www.bioconductor.org/biocLite.R") biocLite("AnnotationDbi") which will ensure you have the correct version, and will install dependencies as well. If you want to be doubly sure, you can pass a character vector of c("AnnotationDbi","DBI") to biocLite(). Best, Jim > > [[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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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@omar-gutierrez-arenas-4624
Last seen 7.1 years ago
Dear Colleagues, I'm using redefined cdf from GATExplorer to analyse microarray data. They work OK with rma, but they don't with gcrma. Does this have an easy solution? Bellow you can see commands and messages. > dtst <- ReadAffy() > dtst@cdfName <- "genemappermouse4302" > pdtst <- gcrma(dtst) Adjusting for optical effect......Done. Computing affinities[1] "Checking to see if your internet connection works..." [1] "Environment genemappermouse4302probe was not found in the Bioconductor repository." Error in get(probepackagename) : object 'genemappermouse4302probe' not found > affinfo <- compute.affinities("genemappermouse4302") Computing affinities[1] "Checking to see if your internet connection works..." [1] "Environment genemappermouse4302probe was not found in the Bioconductor repository." Error in get(probepackagename) : object 'genemappermouse4302probe' not found > pdtst <- rma(dtst) Background correcting Normalizing Calculating Expression > Looking forward, Omar [[alternative HTML version deleted]]
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Hi Omar, On 5/5/2011 7:01 AM, Omar Gutierrez Arenas wrote: > Dear Colleagues, > > I'm using redefined cdf from GATExplorer to analyse microarray data. They > work OK with rma, but they don't with gcrma. Does this have an easy > solution? Bellow you can see commands and messages. Please don't hijack existing threads. If you have a new question, send a new email. As for the solution, you could ask the GATExplorer people to create the required probe packages. Or you could use the MBNI remapped cdf packages, which have corresponding probe packages. Best, Jim > >> dtst<- ReadAffy() > >> dtst at cdfName<- "genemappermouse4302" > >> pdtst<- gcrma(dtst) > Adjusting for optical effect......Done. > Computing affinities[1] "Checking to see if your internet connection > works..." > [1] "Environment genemappermouse4302probe was not found in the Bioconductor > repository." > Error in get(probepackagename) : > object 'genemappermouse4302probe' not found > >> affinfo<- compute.affinities("genemappermouse4302") > Computing affinities[1] "Checking to see if your internet connection > works..." > [1] "Environment genemappermouse4302probe was not found in the Bioconductor > repository." > Error in get(probepackagename) : > object 'genemappermouse4302probe' not found > >> pdtst<- rma(dtst) > Background correcting > Normalizing > Calculating Expression >> > > Looking forward, > > Omar > > [[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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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