Skip Navigation



Bioinformatics Advance Access published online on January 17, 2006
Bioinformatics, doi:10.1093/bioinformatics/btk047
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
22/7/802    most recent
btk047v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Piepho, H. P.
Right arrow Articles by Hochholdinger, F.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Piepho, H. P.
Right arrow Articles by Hochholdinger, F.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 9, 2005
Revised December 22, 2005
Accepted January 6, 2006

Article

Combining signals from spotted cDNA microarrays obtained at different scanning intensities

H. P. Piepho 1 *, B. Keller 1, N. Hoecker 2, and F. Hochholdinger 2

1 Bioinformatics Unit, Institute for Crop Production and Grassland Research, University of Hohenheim, Fruwirthstr. 23, 70599 Stuttgart, Germany
2 Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany

* To whom correspondence should be addressed.
H. P. Piepho, E-mail: piepho{at}uni-hohenheim.de


  Abstract

Motivation: The analysis of spotted cDNA microarrays involves scanning of color signals from fluorescent dyes. A common problem is that a given scanning intensity is not usually optimal for all spotted cDNAs. Specifically, some spots may be at the saturation limit, resulting in poor separation of signals from different tissues or conditions. The problem may be addressed by multiple scans with varying scanning intensities. Multiple scanning intensities raise the question of how to combine different signals from the same spot, particularly when measurement error is not negligible.

Results: This paper suggests a nonlinear latent regression model for this purpose. It corrects for biases caused by the saturation limit and efficiently combines data from multiple scans. Combining multiple scans also allows reduction of technical error particularly for cDNA spots with low signal. The procedure is exemplified using cDNA expression data from maize.

Availability: All methods were implemented using standard procedures available in the SAS/STAT module of the SAS System. Programming statements are available from the first author upon request.

Associate Editor: Steen Knudsen
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 GeneticsHome page
N. Hoecker, B. Keller, N. Muthreich, D. Chollet, P. Descombes, H.-P. Piepho, and F. Hochholdinger
Comparison of Maize (Zea mays L.) F1-Hybrid and Parental Inbred Line Primary Root Transcriptomes Suggests Organ-Specific Patterns of Nonadditive Gene Expression and Conserved Expression Trends
Genetics, July 1, 2008; 179(3): 1275 - 1283.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.