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An ANOVA model including the following terms as fixed sources of variance: Type (population, the term of interest), Dye (Fluorescent dye) and Sample (biological sample) while Array (individual microarray) was included as random term.
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10% of the measurable genes on rice microarray were included in their network.
Furthermore, 32% of the features corresponding to PPR proteins on the microarray were included in the trend set.
The complete sequences of the genes represented on the microarray were included on the platform submission to GEO.
We amplified 250 ng of RNA, which was converted to cRNA using the Illumina TotalPrep-96 RNA Amplification kit (Ambion, Carlsbad, CA, USA): 750 ng of cRNA was used for hybridization onto the Illumina Whole-Genome Gene Expression Direct Hybridization microarray (Illumina, San Diego, CA, USA), and 25,559 probes from the microarray were included for analysis.
Likewise, supplementary pre-processed data (i.e., analyzed by original study researchers) from a study using a novel approach (polony multiplex analysis of gene expression, or PMAGE), which is designed to achieve a much higher level of sensitivity than traditional gene expression microarrays, was included.
Only "present" probes in microarrays were included.
In order to minimize errors and the occurrence of false positives, only genes that were expressed at detectable levels in at least 115 arrays of the quality tested 117 microarrays were included in the data analysis.
For correlations, results from 357 microarrays were included.
For citrus canker, all microarrays are included in the leaves group.
Only Affymetrix HG-U133A microarrays were included for full comparability of all the probes on the arrays.
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