[BioC] reading Agilent Feature Extraction files with Limma

Axel.Klenk at Actelion.Com Axel.Klenk at Actelion.Com
Tue Jan 13 10:27:52 CET 2009

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
Gordon Smyth was kind enough to provide a solution that you can find here:



 - axel

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

             Remi Gagne                                                    
             <remi_gagne at hc-sc                                             
             .gc.ca>                                                    To 
             Sent by:                  bioconductor at stat.math.ethz.ch      
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             ces at stat.math.eth                                             
             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( with read.maimages and always
have a few features missing. The arrays are 4x44k whole mouse genome

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.


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