Question: results.summary does not recognize annotations
0
gravatar for Peter Schjerling
10.9 years ago by
Peter Schjerling10 wrote:
Hi, I have a problem with getting results.summary to recognize the annotation files. If I write: > summary <- results.summary(significant, "hgu95av2") I get: > Error in library(cdfname, character.only = TRUE) : there is no package called 'hgu95av2' I have loaded the library (hgu95av2.db) and if I for instance write: > mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="" ))) I get the correct annotation "TIE1". I have made a simple test script which result in the error above: library(simpleaffy) library(hgu95av2.db) library(estrogen) datadir <- system.file("extdata", package = "estrogen") setwd(datadir) pd <- read.AnnotatedDataFrame("estrogen.txt", header = TRUE, sep = "", row.names=1) raw.data <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose=T) x.mas5 <- call.exprs(raw.data,"mas5") results <- pairwise.comparison(x.mas5, "estrogen", spots=raw.data) significant <- pairwise.filter(results, min.exp=log2(100), min.exp.no=4, min.present.no=4, present.by.group=T, fc=log2(1.3), tt=0.05) cdfName(raw.data) cleancdfname(cdfName(raw.data)) mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="" ))) summary <- results.summary(significant, "hgu95av2") I guess it have something to do with the new ".db" format as it used to work with an older version of R and Bioconductor. The version I use now is R 2.8.0 and updated Bioconductor libraries. Am I just making some stupid error here as I have been unable to find any references to similar problems on the net? Best regards, Peter Schjerling
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ADD COMMENTlink modified 10.9 years ago by anna freni sterrantino120 • written 10.9 years ago by Peter Schjerling10
Answer: results.summary does not recognize annotations
0
gravatar for Jenny Drnevich
10.9 years ago by
Jenny Drnevich1.9k
United States
Jenny Drnevich1.9k wrote:
HI Peter, Like Jim, I thought you should just try: > summary <- results.summary(significant, "hgu95av2.db") But thanks to your reproducible example I got the following error: Error in get(paste(cdfname, "SYMBOL", sep = "")) : variable "hgu95av2.dbSYMBOL" was not found So it does look like there is an error somewhere in the results.summary code - it now needs to strip off the .db from the cdfname before pasting on "SYMBOL" etc. HTH, Jenny At 08:30 AM 11/13/2008, Peter Schjerling wrote: >Hi, > >I have a problem with getting results.summary to recognize the >annotation files. > >If I write: > > summary <- results.summary(significant, "hgu95av2") >I get: > > Error in library(cdfname, character.only = TRUE) : > there is no package called 'hgu95av2' > >I have loaded the library (hgu95av2.db) and if I for instance write: > > mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="" ))) >I get the correct annotation "TIE1". > >I have made a simple test script which result in the error above: > >library(simpleaffy) >library(hgu95av2.db) >library(estrogen) >datadir <- system.file("extdata", package = "estrogen") >setwd(datadir) >pd <- read.AnnotatedDataFrame("estrogen.txt", header = TRUE, sep = >"", row.names=1) >raw.data <- ReadAffy(filenames = rownames(pData(pd)), phenoData = >pd, verbose=T) >x.mas5 <- call.exprs(raw.data,"mas5") >results <- pairwise.comparison(x.mas5, "estrogen", spots=raw.data) >significant <- pairwise.filter(results, min.exp=log2(100), >min.exp.no=4, min.present.no=4, present.by.group=T, fc=log2(1.3), tt=0.05) >cdfName(raw.data) >cleancdfname(cdfName(raw.data)) >mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="" ))) >summary <- results.summary(significant, "hgu95av2") > > >I guess it have something to do with the new ".db" format as it used >to work with an older version of R and Bioconductor. The version I >use now is R 2.8.0 and updated Bioconductor libraries. > >Am I just making some stupid error here as I have been unable to >find any references to similar problems on the net? > >Best regards, >Peter Schjerling > >_______________________________________________ >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 Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu
ADD COMMENTlink written 10.9 years ago by Jenny Drnevich1.9k
Answer: results.summary does not recognize annotations
0
gravatar for James W. MacDonald
10.9 years ago by
United States
James W. MacDonald51k wrote:
Hi Peter, Have you tried results.summary(significant, "hgu95av2.db") ? Best, Jim Peter Schjerling wrote: > Hi, > > I have a problem with getting results.summary to recognize the > annotation files. > > If I write: > > summary <- results.summary(significant, "hgu95av2") > I get: > > Error in library(cdfname, character.only = TRUE) : > there is no package called 'hgu95av2' > > I have loaded the library (hgu95av2.db) and if I for instance write: > > mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="" ))) > I get the correct annotation "TIE1". > > I have made a simple test script which result in the error above: > > library(simpleaffy) > library(hgu95av2.db) > library(estrogen) > datadir <- system.file("extdata", package = "estrogen") > setwd(datadir) > pd <- read.AnnotatedDataFrame("estrogen.txt", header = TRUE, sep = "", > row.names=1) > raw.data <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, > verbose=T) > x.mas5 <- call.exprs(raw.data,"mas5") > results <- pairwise.comparison(x.mas5, "estrogen", spots=raw.data) > significant <- pairwise.filter(results, min.exp=log2(100), min.exp.no=4, > min.present.no=4, present.by.group=T, fc=log2(1.3), tt=0.05) > cdfName(raw.data) > cleancdfname(cdfName(raw.data)) > mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="" ))) > summary <- results.summary(significant, "hgu95av2") > > > I guess it have something to do with the new ".db" format as it used to > work with an older version of R and Bioconductor. The version I use now > is R 2.8.0 and updated Bioconductor libraries. > > Am I just making some stupid error here as I have been unable to find > any references to similar problems on the net? > > Best regards, > Peter Schjerling > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
ADD COMMENTlink written 10.9 years ago by James W. MacDonald51k
Answer: results.summary does not recognize annotations
0
gravatar for anna freni sterrantino
10.9 years ago by
anna freni sterrantino120 wrote:
Hi Peter, If I understood what you mean, you may want to try mget(significant, hgu95av2SYMBOL) well of course significant is a vector of characters Best Regards Anna Anna Freni Sterrantino Ph.D Student Department of Statistics University of Bologna, Italy via Belle Arti 41, 40124 BO. ________________________________ Da: Peter Schjerling <peter@mrna.dk> A: bioconductor@stat.math.ethz.ch Inviato: Giovedì 13 novembre 2008, 15:30:39 Oggetto: [BioC] results.summary does not recognize annotations Hi, I have a problem with getting results.summary to recognize the annotation files. If I write: > summary <- results.summary(significant, "hgu95av2") I get: > Error in library(cdfname, character.only = TRUE) : there is no package called 'hgu95av2' I have loaded the library (hgu95av2.db) and if I for instance write: > mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="" ))) I get the correct annotation "TIE1". I have made a simple test script which result in the error above: library(simpleaffy) library(hgu95av2.db) library(estrogen) datadir <- system.file("extdata", package = "estrogen") setwd(datadir) pd <- read.AnnotatedDataFrame("estrogen.txt", header = TRUE, sep = "", row.names=1) raw.data <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose=T) x.mas5 <- call.exprs(raw.data,"mas5") results <- pairwise.comparison(x.mas5, "estrogen", spots=raw.data) significant <- pairwise.filter(results, min.exp=log2(100), min.exp.no=4, min.present.no=4, present.by.group=T, fc=log2(1.3), tt=0.05) cdfName(raw.data) cleancdfname(cdfName(raw.data)) mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="" ))) summary <- results.summary(significant, "hgu95av2") I guess it have something to do with the new ".db" format as it used to work with an older version of R and Bioconductor. The version I use now is R 2.8.0 and updated Bioconductor libraries. Am I just making some stupid error here as I have been unable to find any references to similar problems on the net? Best regards, Peter Schjerling _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Unisciti alla community di Io fotografo e video, il nuovo corso di fotografia di Gazzetta dello sport: [[alternative HTML version deleted]]
ADD COMMENTlink written 10.9 years ago by anna freni sterrantino120
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