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The microarrays were scanned by making use of an Innopsys 710A microarray scanner.
This so called "common reference" experimental design for microarray makes use of a species-specific pool of RNA as a common technical reference, and was chosen as it potentially facilitates an extension of this study to other time-points and conditions, if needed (see [ 35], Methods and Additional file 1: Figure S2 for details).
The present microarray meta analysis makes use of the latest methods for microarray data integration and classification.
In order to be consistent throughout our own studies, which made use of the Affymetrix U74Av2 microarrays we made use of data measured using the same microarrays.
In this article, we focus on the ArrayExpress Archive (1) that makes use of microarray standards.
To make use of the microarray expression data, we use the original microarray data [ 24, 25].
The 12-plex Nimblegen platform was selected to make use of newer microarray technology.
Second, global transcriptome analysis in mussels could make use of specie-specific microarray platforms.
Dye-swap normalisation makes use of reverse labelling in the two microarray replicates directly [ 26].
In this work, we have made use of a novel customised Pinus taeda microarray.
For example, most classification and regression methods for microarray data are based on the whole set of genes and have not made use of pathway information.
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