[BioC] hgu133plus2cdfSYMBOL not found

Tony McBryan tony at mcbryan.co.uk
Mon Dec 14 11:49:45 CET 2009


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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