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 [[alternative HTML version deleted]]

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/1 1148 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 [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com