The microarray-based classification of Δtag and ΔdinG cells as depleted after MMS exposure, contrary to plate-based methods, led to the discovery that Δtag and ΔdinG cells show a filamentation phenotype after MMS exposure, thus accounting for the discrepancy.
To validate the microarray method using more complex polymeric samples, CBM20 screening was performed using CoMPP arrays populated with extracts from developing and germinating barley grain28,29.
However, the digital counting of sequence tags in HTS methods leads to a different observation of noise process compared with the analog measurement of probe intensity in microarrays.
Microarray methods were modified from [ 92].
The high-throughput of microarray technology has led to explosion of data concerning the expression levels of the genes but most of statistical methods such as fold change and t-test identify genes with significant changes.
Despite the conflicting information given by a handful of early published studies where both concordance[7] [9] and discordance[10] [12] between technologies was demonstrated, the maturation of microarray technology and data analysis methods has led to improved cross-platform correlations[6], [13].
It is expected that revisiting the microarray data with our method could lead to the discovery of new biological knowledge and new insight into mechanisms for old biological processes and diseases.
It is also clear that varying the microarray platform, reference sample or segmentation method used for microarray image analysis leads to significant differences in data repeatability and gene discovery [ 16- 18].
To identify significant microRNAs based on differential expression changes across time, we used significance analysis of microarrays method, adapted for small RNA-sequencing data (SAMSeq 41.
Most often, those methods — capable of probing only specific, limited regions of the genome arising from a type of experiment called DNA microarrays — led to the exclusive scrutiny of regions called promoters nestled near the start of the gene.
