Hi, I get the following error when running gpQuality > gpQuality() [1] "Starting gpQuality..." Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed In addition: Warning messages: 1: input string 30 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) 2: input string 30 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) The following is package description on my machine: > packageDescription("arrayQuality") Package: arrayQuality Version: 1.12.0 Date: 2007-04-19 Title: Assessing array quality on spotted arrays Depends: R (>= 2.2.0), marray, limma, convert, hexbin, gridBase, RColorBrewer biocViews: Microarray,TwoChannel,QualityControl,Visualization Suggests: mclust, MEEBOdata, HEEBOdata Author: Agnes Paquet and Jean Yee Hwa Yang <yeehwa at="" stat.berkeley.edu=""> Maintainer: Agnes Paquet <paquetagnes at="" yahoo.com=""> Description: Functions for performing print-run and array level quality assessment. License: LGPL URL: http://arrays.ucsf.edu/ Packaged: Wed Apr 25 01:56:01 2007; biocbuild Built: R 2.5.0; ; 2007-07-06 13:04:04; unix I have faced the same error with agQuality but not with maQualityPlots functions. I suspect this is file reading error. Thanks for the help, -- Shripad Sinari Computer Database Specialist Bioinformatics Shared Service Arizona Cancer Center Tucson, Arizona, 85725-5024

Hi Shripad, What kind of arrays are you working with? arrayQuality provides different functions for different types of arrays, and you will need to use the one that matches the arrays your are analyzing. gpQuality is expecting two-color microarray in the .gpr file format from GenePix, and agQuality is taking Agilent files in a .txt format. You mentionned that you were able to use maQualityPlots, could you please email me the R code you used to read in the array files, then call the function, so that I can check how it differs from arrayQuality? Best, Agnes ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Shripad Sinari Sent: Thu 7/19/2007 11:43 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Error with arrayQuality Hi, I get the following error when running gpQuality > gpQuality() [1] "Starting gpQuality..." Error in if (skip > 0) readLines(file, skip) : missing value where TRUE/FALSE needed In addition: Warning messages: 1: input string 30 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) 2: input string 30 is invalid in this locale in: grep(pattern, x, ignore.case, extended, value, fixed, useBytes) The following is package description on my machine: > packageDescription("arrayQuality") Package: arrayQuality Version: 1.12.0 Date: 2007-04-19 Title: Assessing array quality on spotted arrays Depends: R (>= 2.2.0), marray, limma, convert, hexbin, gridBase, RColorBrewer biocViews: Microarray,TwoChannel,QualityControl,Visualization Suggests: mclust, MEEBOdata, HEEBOdata Author: Agnes Paquet and Jean Yee Hwa Yang <yeehwa at="" stat.berkeley.edu=""> Maintainer: Agnes Paquet <paquetagnes at="" yahoo.com=""> Description: Functions for performing print-run and array level quality assessment. License: LGPL URL: http://arrays.ucsf.edu/ Packaged: Wed Apr 25 01:56:01 2007; biocbuild Built: R 2.5.0; ; 2007-07-06 13:04:04; unix I have faced the same error with agQuality but not with maQualityPlots functions. I suspect this is file reading error. Thanks for the help, -- Shripad Sinari Computer Database Specialist Bioinformatics Shared Service Arizona Cancer Center Tucson, Arizona, 85725-5024 _______________________________________________ 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

Shripad Sinari <shripad at="" email.arizona.edu=""> writes: > Hi, > > I get the following error when running gpQuality > > > gpQuality() > [1] "Starting gpQuality..." > Error in if (skip > 0) readLines(file, skip) : > missing value where TRUE/FALSE needed > In addition: Warning messages: > 1: input string 30 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > 2: input string 30 is invalid in this locale in: grep(pattern, x, > ignore.case, extended, value, fixed, useBytes) > Please include sessionInfo() output. This looks like a locale issue. Perhaps retry using the "C" locale. apropos("locale") + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org