For comparison with the MANOVA, we also fitted two-way ANOVA models separately for every immunological response using the aov function in R. In particular, for each day, response and effect, we computed F-based p-values.
Briefly, experiments were analyzed under a Type-I Anova with two fixed factors and equal replication, using the aov function in R: aov(Attacks∼Color×Jelly, data=d.f .. Plots were generated using ggplot2 (Wickham, 2009).
All analyses were performed in R 2.10.1 (The R Foundation for Statistical Computing 2009) using the aov function and type II sums of squares.
For parametric tests ANOVA and post hoc Tukey honest significant difference (HSD) tests were carried out by using the "aov" and "TukeyHSD" functions.
ANOVA was done using the aov function in the stats package of R, and box plots were drawn with R. Statistically significant changes are marked with asterisks in the figures.
The ratios of the other measurements were analyzed using the aov function in R, and the proportion of variance explained determined as the square of the residuals of the strain factor over the total sum of squares.
One-way ANOVA on the log2-transformed expression ratios (treated versus control) with the factor time was applied using the aov function in the statistical software R utilizing partitioned error for replicates.
Two-way ANOVA was also performed for non-targeted GCxGC-TOFMS data using the aov function of the stats package in R statistical programming language (http://www.r-project.org).org
We compared average larval masses across plant genotypes for each cohort (days 3 and 5) also using an ANCOVA (using the aov function in the statistical package R v. 2.15.0) to test for effects of crowding on larval growth rates as there were multiple larvae per plant.
To determine the significance and variances of features (see question a), the t-test of the Perl CPAN package Statistics::TTest (Juan, 2003) and Statistics::KruskalWallis (Lee, 2003) is offered as well as analysis of variance using the aov method of the R statistical software (R Development Core Team, 2011), which fits a linear model.
Stitch using the sewing machine.
