[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
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
.gc.ca> To
Sent by: bioconductor at stat.math.ethz.ch
bioconductor-boun cc
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(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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