[BioC] reading Agilent Feature Extraction files with Limma

[Axel.Klenk at Actelion.Com]

Dear Remi,

there is no problem with read.maimages() -- Agilent is spreading a number
of blank
spots over its arrays so that nRows * nColumns != nSpots...

Interestingly, these blank spots have a row of type "ignore" in the
annotation files
distributed on their DVDs and web site (if you manage to find them there
:-)) but not in
the FES output files which contain only 45,018 rows of intensity data.

However, this will cause problems when you're trying to use functions
assuming and
checking for a complete data matrix such as limma's imageplot() -- for this
case,
Gordon Smyth was kind enough to provide a solution that you can find here:

http://article.gmane.org/gmane.science.biology.informatics.conductor/11148

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
Switzerland
phone +41 61 565 6367 / fax +41 61 565 6470 / axel.klenk at actelion.com /
www.actelion.com



                                                                           
             Remi Gagne                                                    
             <remi_gagne at hc-sc                                             
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             Sent by:                  bioconductor at stat.math.ethz.ch      
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             z.ch                                                  Subject 
                                       [BioC] reading Agilent Feature      
                                       Extraction files with Limma         
             13.01.2009 04:31                                              
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           




Dear all,

I've been trying to read FE files v(9.5.3.1) with read.maimages and always
have a few features missing. The arrays are 4x44k whole mouse genome
arrays(Agilent-014868).

My file contains 45 220 features and only 45 018 features from each file
gets loaded.

I have tried the last stable version of R 2.8.1 with the according
Bioconductor package and also the development version of R and
Bioconductor without success.

The compressed file from the FE is 16Mb, a little to big to post.

I would like know if other users have experienced this issue. If you are
interested in getting a copy of a file, let me know.

Thanks,

Remi
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