Using group data analysis (M-statistics), we detected increased binding to select arrayed proteins by IgM from the day 6 sera compared to the day -1 sera across all animals in the group, while IgG interactions with the orthopox proteins were negligible.
Subjects from the replication panel were further genotyped by sequence enrichment of the 12p13.2 locus on Sure Select arrays (Agilent Inc., Santa Clara, CA, USA) followed by HiSEQ (Illumina Inc).
CEBS users can select arrays corresponding to one or more compounds from the library and use knowledge base tools to identify genes with significantly changed transcript levels.
Because signal intensities can affect reproducibility, we maximized signals by selecting array elements that were less than 2.5 kbp from the gene ends (see Methods).
The strand specificity was also evident with genes for non-coding RNAs where we selected array elements for both orientations (Table 1).
The maximum height of the hook-plot reflects the relevant 3′/5′-intensity gradient of the selected array enabling the unbiased comparison of differentially expressed genes under variable RNA quality.
The quantiles of distributions for both metrics for selected array types are available as supplementary material and can be used to evaluate the quality level of any new microarray experiment.
We selected array positions that had significant fold ratios (P <0.05) and mean log2 fold change ratios ≤ −0.25 and ≥0.25 (emphasized in the Volcano plots in Figure 1) which corresponded to actual fold changes of <0.84 and >1.19, respectively.
We selected arrays and genes with greater than 75% good data (representing the amount of data passing the spot criteria).
Currently, three major commercial products, namely, Nimblegen's SeqCap (array-based and solution-based), Illumina's TruSeq (solution-based), and Agilent's Sure-Select (array-based and solution-based), are used in combination with NGS platforms (e.g., Illumina, Roche 454, and Solid) to achieve efficient target enrichment.
All selected arrays were human cancer samples hybridized onto genome-wide array platforms.
