Figures of the whole genome comparison were generated using BRIG (BLAST Ring Image Generator) [ 54] and Easyfig [ 25].
That is possibly because the gene expression profiles under comparison were generated under different conditions, such as different tissue samples, cell lines/types, treatment doses and time durations, disease/development stages, ages, genotypes/variations, and experiment protocols etc.
A list of candidate genes resulting from the two-way (T2Bo_vir and _att only) comparison was generated for further evaluations.
The Latin Square data set used for comparison was generated by scientists at Affymetrix and is available from the company's website [ 38].
A volcano plot for each comparison was generated that displays the negative log10-transformed p-value versus log2-transformed fold change for each array locus.
A multipoint dissolution profile comparison was generated between the mesalamine capsules and tablets over a range of pH values (pH 4.5, 6.0, 6.8, 6.8, 7.2, and 7.5).
A second set of FPKM values enabling cross-species comparison were generated for contigs of interest through multiplication of the first, library-specific FPKM values by respective scaling factors.
The random allocation sequence for each comparison was generated by using a specific function (-ralloc-) in Stata (StataCorp, College Station, TX) software within the clinical unit using randomly varying block sizes of two, four, and six.
Significant gene expression changes for all but the LNCaP 3 day xenograft comparison were generated based on ANOVA adjusted p-values of 0.05 corrected for multiple testing effects using Benjamini-Hochberg FDR and fold changes of at least 1.3.
