[BioC] Error with arrayQuality

[Paquet, Agnes]

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 at 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

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