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When two or more probes assigned the same gene name gave the same pattern of regulation across the seven microarray comparisons, they were deemed to be redundant probes (as indicated by assignment to the same total flag sum (TFS) group; see Additional file 2 and below), and only the probe with the lowest set of p-values was retained.
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The composite dataset incorporated 232 microarray comparisons of RNA samples by single or dual microarray platforms, cDNA or oligonucleotide based probes, and human or mouse sequence information.
This conclusion is supported by microarray comparisons of strain-dependent differences in host gene expression [12].
Microarray comparisons of adult retinas showed little consistency with expression changes found in P4 retina.
Only those array features which were significantly 'increased' or 'decreased' in three out of three microarray comparisons were considered to have met our criteria for inclusion in the low stringency datasets.
All microarray comparisons were made with at least 3 animals in each condition, and only those genes having at least 2-fold difference and whose coefficient of variance was less than 100% were considered to be differentially expressed.
Expression microarray comparisons of strains MGAS2221 and 2221ΔPEL were performed using RNA isolated from triplicate cultures of each strain grown in THY broth at both the exponential and stationary phases of growth.
All microarray comparisons were performed in quadruplicates using dye swaps performed on the same RNA extraction (thus 4 arrays were used per sample class derived from two separate RNA extractions).
Microarray comparisons.
The development of predictors began with individual microarray comparisons using the liver tissue.
RT-qPCR was used to validate the DEGs identified in the microarray comparisons.
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