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GH also did microarray data extraction.
AM, LR, IL, AC performed the microarray data extraction, statistical analysis and interpretation of data.
Quality control of the hybridisation, microarray data extraction and initial analysis were carried out using the Illumina BeadStudio software (Illumina, Inc., San Diego, CA).
For 8 of the contigs higher expressed in the toxic strains, the signals of the non-toxic strain were identified as not "well above background" by the microarray data extraction software on at least 8 of the 12 arrays, and on at least one array for each strain-time-point combination.
Quality control of the hybridisation, microarray data extraction and initial analysis were carried out using the Illumina BeadStudio software (Illumina, Inc .. Outlier samples were removed via hierarchical clustering analysis provided by the Illumina BeadStudio software and also using the TIGR MeV software (Institute for Genomic Research, Rockville, MD, USA), via different distance metrics.
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After hybridization for 17 hours the arrays were washed and scanned using an Agilent scanner and microarray data extracted with Agilent Feature Extraction software.
MA wrote the manuscript, designed the microarray study, carried out microarray hybridizations, data extraction and analysis.
CRV designed the microarray study, participated in microarray hybridizations, data extraction and analysis, coordination, and wrote the manuscript.
During programming, we took into account that for many microarray data users, extraction of global expression patterns of single genes or gene families can be time-consuming and its visualization difficult.
JS carried out microarray hybridizations, data extraction and analyses, and wrote the manuscript.
Microarray data was extracted with Agilent's Feature Extraction software (version 5.1) and analyzed using the Limma package of Bioconductor.
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