Here we considered that a gene was expressed if any of the probes detecting that gene in the microarray was called as 'expressed' according to the Barcode method.
A single discrepancy was found among the five microarrays: two of the microarrays were called 'G ', matching the reference sequence, two others were called heterozygotes for 'A' and 'G', and the last microarray showed a no-call in this position.
Genes that were consistently identified as differentially expressed using multiple ranking algorithms [ 84] (fold change ranking, ordinary t-statistic, shrinkage t-statistic, limma, significance analysis of microarrays) were called significant and retained for further analysis.
One extensively used method in microarray data analysis is called SAM for "Significance Analysis of Microarray" [ 2].
In this approach developed by Moretti et al. [ 8], genes serve as players and microarray measurements are called cooperative games.
Microarray entries are called 'samples' and are grouped into 'series' that are essentially experiments that comprise groups of samples in a study.
The selected threshold resulted in 1410 microarray features being called significant with a median FDR = 0.3% and 90th percentile FDR = 0.5%.
Of the 34 strains, 18 had corresponding 5'UTR sequences tiled on the microarray and were called prototype serotypes, which were used to verify the accuracy of the designed HRV probes.
Among all probe sets on the wheat microarray, 17,134 were called "present" in all samples and 4,768 probe sets showed a level of expression, normalized to the corresponding probe set median, between 0.66 and 1.5 indicating that the corresponding mRNA showed less than 1 fold change variation in their expression across all samples.
The remaining two thirds were either not inferred as differentially regulated from GeneChip microarray data, or were called differentially regulated but in the opposite direction.
