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If the interaction effect τψ is insignificant after multiple-test correction (as we used FDR ≤ 0.01, Benjamini-Hochberg Procedure [ 25]), we then report P-values of the treatment effect τ; otherwise we consider sibling probe sets as independent probe sets.

To provide a first-order cut at many of the engineering realities associated with such a mission, we consider a probe that can be launched with available vehicles and infrastructure.

We considered a probe absent if it had more than one absent call among the infected animals and more than one absent call among the uninfected animals.

We considered only probe sets that were present in both array types U133a and U133plus2.

To minimize false positives we considered only probe sets that presented similar statistically significant variations (Fold change >1,5; FDR<1%) for both time points (3 days and 40 days).

We considered any probe that did not fall into an exon marked as "confirmed" by WormBase to be in the null distribution.

Using this search, if a probe sequence hit only a single region in the genome we considered the probe to be present as a single copy in the genome.

For type II probes that contained Rs we considered two probe sequence versions, one with all Rs replaced by As and the other with all Rs replaced by Gs.

When the averaged signal intensity from hybridization was higher than both two standard values, background value (negative samples and blank control plus 3x SD) and cutoff value (15% of biotinylated control value), we considered the probe as true signal.

We considered a probe unmethylated if the β-value was ≤ 0.15 and hypermethylated if the individual tumor had a β-value at least 0.2 higher than the β-value of the matched normal sample.

We considered a probe set as expressed in a tissue, if its perfect match versus mismatch signal distributions was lower or equal 0.05 in at least one of the two chip experiments.

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