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Each scatter plot shows RPKM in mRNA-Seq and the signal intensity (average of three biological replicates) for the microarray of the roots.
We used analysis of variance (ANOVA), t-score analysis and SAM (Significant Analysis of Microarray) of the J-Express program package for identification of differentially expressed genes.
Inclusion in this microarray of the coding sequences within the four CJIEs, identified initially in strain RM1221 [40], [43], differentiated the South African HS∶41 strains from the two closely-related HS∶41 strains from Mexico.
Hybridization with target DNA prepared from a single genotype generated a single block of intensive hybridization corresponding to the location on the microarray of the tiling path for that genome (e.g. hybridizations with the T30 and the T36 target DNA in Fig. 2).
One of the first works on the analysis of a gene expression microarray dataset for yeast was presented by Eisen et al. [43], which is among the most cited works in microarray of the Saccharomyces cerevisiae (a highly cited contribution as reported by Google Scholar and ISI Web of knowledge figures of 10,054 and 6,963, respectively).
To define these sets we used the microarray of the four pure cell types.
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Upon rigorous examination of the resulting diagnostic plots, 116 microarrays of the supreme quality were taken for the further analysis.
Note that just this type of self-complementary mismatches was selected to design MM probes on microarrays of the GeneChip-type.
High-throughput approaches based on microarrays of the vaccinia virus proteome were recently used to identify or confirm individual viral proteins associated with smallpox immunity [14], [16].
In addition, all scaffolds of the whole-genome tiling microarray design were randomly distributed over the 5 microarrays of the array set to prevent that any single microarray features all the small scaffolds.
Within groups, microarrays of the same treatment were clustered together.
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