[BioC] hgu133plus2cdfSYMBOL not found
Groot, Philip de
philip.degroot at wur.nl
Mon Dec 14 13:29:42 CET 2009
Dear Tony,
Yes, I was already afraid for this. simpleaffy is not updated to properly handle the .db annotation packages. In the past (5 R-versions ago), a annotation library was loaded by the command:
library(hgu133plus2)
However, nowadays it should be loaded by:
library(hgu133plus2.db)
Unfortunately, things go wrong in the get.annotation function (simpleaffy), which reads like this:
> get.annotation
function (x, cdfname, verbose = FALSE)
{
library(cdfname, character.only = TRUE)
symb <- .strip.list(mget(x, envir = get(paste(cdfname, "SYMBOL",
sep = "")), ifnotfound = list(.if.probeset.not.found)))
desc <- .strip.list(mget(x, envir = get(paste(cdfname, "GENENAME",
sep = "")), ifnotfound = list(.if.probeset.not.found)))
accno <- .strip.list(mget(x, envir = get(paste(cdfname, "ACCNUM",
sep = "")), ifnotfound = list(.if.probeset.not.found)))
uni <- .strip.list(mget(x, envir = get(paste(cdfname, "UNIGENE",
sep = "")), ifnotfound = list(.if.probeset.not.found)))
ok <- (symb != "NoAnno") & (desc != "NoAnno") & (accno !=
"NoAnno") & (uni != "NoAnno")
names(ok) <- x
if (!ok && verbose) {
warning(paste("value for '", names(ok)[ok], "' not found",
sep = ""), call. = FALSE)
}
acc.lnk <- paste("=HYPERLINK(\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&term=",
accno, "\",\"", accno, "\")", sep = "")
acc.lnk[!ok] <- "NoAnno"
uni.lnk <- paste("=HYPERLINK(\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=unigene&term=",
uni, "&dopt=unigene\",\"", uni, "\")", sep = "")
uni.lnk[!ok] <- "NoAnno"
res <- cbind(symb, acc.lnk, uni.lnk, desc)
res[res == "NoAnno"] <- "No Annotation Found"
colnames(res) <- c("gene name", "accession", "unigene", "description")
return(res)
}
<environment: namespace:simpleaffy>
The top line of this function loads the library (without .db extension) and hence either loading the library will fail or getting the annotation will fail. Copying this text into a new function and deleting the top-line will fix your problem. Provided that you load the .db library first.
Regards,
Dr. Philip de Groot Ph.D.
Bioinformatics Researcher
Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail: Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl>
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/>
http://humannutrition.wur.nl <http://humannutrition.wur.nl/>
https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/>
________________________________
From: Tony McBryan [mailto:tony at mcbryan.co.uk]
Sent: Mon 14-12-2009 12:35
To: Groot, Philip de; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] hgu133plus2cdfSYMBOL not found
Hello Philip,
I have applied the change as you suggested but I'm afraid it still fails
at the same location; although the content of the error message has
changed slightly and now reads:
---
Error in library(cdfname, character.only = TRUE) :
there is no package called 'hgu133plus2'
---
Thank you for your previous extremely quick response,
Tony
Groot, Philip de wrote:
> Hello Tony,
>
> object 'hgu133plus2cdfSYMBOL' should be object 'hgu133plus2SYMBOL' .
>
> Please use:
> summary <- results.summary(pc,cleancdfname(cdfName(raw.data), addcdf=FALSE))
> ^^^^^^^^^^^^^^
>
> Regards,
>
> Dr. Philip de Groot Ph.D.
> Bioinformatics Researcher
>
> Wageningen University / TIFN
> Nutrigenomics Consortium
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> PO Box 8129, 6700 EV Wageningen
> Visiting Address: Erfelijkheidsleer: De Valk, Building 304
> Dreijenweg 2, 6703 HA Wageningen
> Room: 0052a
> T: +31-317-485786
> F: +31-317-483342
> E-mail: Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl>
> Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> <http://www.nutrigenomicsconsortium.nl/>
> http://humannutrition.wur.nl <http://humannutrition.wur.nl/> <http://humannutrition.wur.nl/>
> https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/> <https://madmax.bioinformatics.nl/>
>
>
>
>
> ________________________________
>
> From: Tony McBryan [mailto:tony at mcbryan.co.uk]
> Sent: Mon 14-12-2009 11:49
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] hgu133plus2cdfSYMBOL not found
>
>
>
> Hello list,
>
> I'm having trouble using part of the affy packages within Bio conductor.
> I have a dozen U133Plus2 microarrays I'm doing a differential analysis
> on. Everything works fine until the pairwise comparison stage where I am
> unable to perform a summary (results.summary()) of the results of the
> comparison. The script terminates with the error message:
>
> ---
> Error in get(paste(cdfname, "SYMBOL", sep = "")) :
> object 'hgu133plus2cdfSYMBOL' not found
> ---
>
> as a result of the call to:
>
> summary <- results.summary(pc,cleancdfname(cdfName(raw.data)))
>
> where pc is the result of "pc <- pairwise.comparison(x.rma, "treatment",
> spots=raw.data )".
>
> The only result I could find on Google was a previous posting to this
> list [1] from 2006 which stated that the "hgu133plus2" package was
> required however this seems unavailable from the package repositories:
>
> ---
> > source("http://www.bioconductor.org/biocLite.R")
> > biocLite("hgu133plus2")
> Using R version 2.10.0, biocinstall version 2.5.8.
> Installing Bioconductor version 2.5 packages:
> [1] "hgu133plus2"
> Please wait...
>
> Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
> argument 'lib' is missing: using
> '/home/mcbryan/R/x86_64-pc-linux-gnu-library/2.10'
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
> package 'hgu133plus2' is not available
> ---
>
> I have however attached the "hgu133plus2.db" (which seems to be
> hgu133plus2's replacement?) "hgu133plus2cdf" and "hgu133plus2probe"
> packages to no additional success.
>
> Vital stats: 64bit Linux (Ubuntu 9.04), R2.10.0 (should be latest from
> "deb http://cran.uk.r-project.org/bin/linux/ubuntu karmic/" repository).
> Bioc installed using Bioclite (and all packages updated to latest
> versions using "update.packages(repos=biocinstallRepos(), ask=FALSE)").
>
> I have attached a short script below which reproduces the error for me
> as well as the output of running that script (including sessionInfo()).
>
> If anyone could provide a prod in the right direction it would very much
> be appreciated.
>
> Tony McBryan
> Beatson Institute for Cancer Research, UK
>
> [1] https://stat.ethz.ch/pipermail/bioconductor/2006-January/011746.html
>
>
> ===
>
> runme.R:
>
> ## load Bioconductor relevant package
> ## limma: define experimental design and perform ratio statistics
> ## affy: CEL file manipulations
> ## affyQCReport: Quality Control Report
>
> library(limma)
> library(simpleaffy)
> library(affy)
> library(affyQCReport)
>
> library(hgu133plus2.db)
> library(hgu133plus2cdf)
> library(hgu133plus2probe)
>
> ## set locations for input and output data files
>
> qcDirectory <- "output/"
> outputDirectory <- "output/"
>
> ## read target file detailing input file names into an object
> ## start with defining the name and location of the target file
> ## then read data into the targets object
>
> ## read in CEL files listed in covdesc into raw affy object
>
> raw.data <- read.affy()
>
> ## compile Affy AC Report
> # Temporarily commented out
> # qcFile <- paste(qcDirectory, "affy_qc_report.pdf", sep="")
> # QCReport(raw.data, file=qcFile)
>
> ## MAS5: present/Marginal/Absent analysis
> ## writing the output to a file
>
> x.mas <- call.exprs(raw.data,"mas5")
> outputFile <- paste(outputDirectory, "MAS5_output.csv", sep="")
> write.exprs(x.mas, outputFile, sep="\t")
>
> ## RMA: probe summary intensity value
>
> x.rma <- call.exprs(raw.data,"rma")
> outputFile <- paste(outputDirectory, "RMA_output.csv", sep="")
> write.exprs(x.rma, outputFile, sep="\t")
>
> ## Pairwise comparison
>
> pc <- pairwise.comparison(x.rma, "treatment", spots=raw.data )
>
> ## ---
> ## Fails on next line
> ## ---
> summary <- results.summary(pc,cleancdfname(cdfName(raw.data)))
>
> ## This is what I wanted to do next
> summaryfile <- paste(outputDirectory,"spreadsheet.csv",summary)
> write.annotation(file=summaryfile,summary)
>
>
> ===
>
> Result of source("runme.R"):
>
> R version 2.10.0 (2009-10-26)
> Copyright (C) 2009 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > source("runme.R")
> Loading required package: affy
> 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: genefilter
> Loading required package: gcrma
> Loading required package: xtable
> Loading required package: affyPLM
> Loading required package: preprocessCore
>
> Attaching package: 'affyPLM'
>
>
> The following object(s) are masked from package:stats :
>
> resid,
> residuals,
> weights
>
> Loading required package: RColorBrewer
> Loading required package: lattice
> Loading required package: AnnotationDbi
> Loading required package: org.Hs.eg.db
> Loading required package: DBI
> Background correcting
> Normalizing
> Calculating Expression
> Error in get(paste(cdfname, "SYMBOL", sep = "")) :
> object 'hgu133plus2cdfSYMBOL' not found
> > sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-pc-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] hgu133plus2probe_2.5.0 hgu133plus2cdf_2.5.0 hgu133plus2.db_2.3.5
> [4] org.Hs.eg.db_2.3.6 RSQLite_0.7-3 DBI_0.2-4
> [7] AnnotationDbi_1.8.1 affyQCReport_1.24.0 lattice_0.17-26
> [10] RColorBrewer_1.0-2 affyPLM_1.22.0 preprocessCore_1.8.0
> [13] xtable_1.5-6 simpleaffy_2.22.0 gcrma_2.18.0
> [16] genefilter_1.28.2 affy_1.24.2 Biobase_2.6.1
> [19] limma_3.2.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0 annotate_1.24.0 Biostrings_2.14.8 grid_2.10.0
> [5] IRanges_1.4.9 splines_2.10.0 survival_2.35-7 tools_2.10.0
>
>
>
>
>
>
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