[Bioc-devel] Error in SlideNamesVec assignment in affylmGUI

2 messages · rcaloger, Keith Satterley

rcaloger

Sun, May 20, 2007 1:12 AM #

Hi,
I am the mantainer of oneChannelGUI. My library is an extension of the 
functions available in affylmGUI.
Today a was doing some testing and I realized the presence of an error 
when I was loading conventional 3'IVT Affymetrix arrays.
During the loading of .CEL files and error occured:
Error in colnames(RawAffyData at exprs) : error in evaluating the argument 
'x' in selecting a method for function 'colnames'

This error is present in line 3062 of main.R of affylmGUI, in function 
OpenCDFandTargetsfiles().
The error is removed if I modify the line to:
Try(SlideNamesVec <- colnames(exprs(RawAffyData)))

Cheers
Raffaele

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
www:   www.bioinformatica.unito.it

Keith Satterley

Mon, May 21, 2007 1:08 AM #

Hi Raffaele,

thanks for the message. I'm aware of this problem and in fact there are some 
other locations in the code that have the similar problems. I have fixed those 
too and the amended version will soon be on Bioc-Devel.

Note that a problem has arisen with PLM normalization. Avoid it at the moment 
until I fix it.

After thorough testing I shall see if I can fix the release version. Sorry about 
the errors,

cheers,

Keith Satterley
Maintainer: affylmGUI

rcaloger wrote: