- WBPaper00041207:CE_dauer_down
The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function. Control of FDR was employed as correction for multiple testing.
Genes dowm regulated in the dauer versus dauer-exit worms.
- WBPaper00041207:CE_dauer_up
The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function. Control of FDR was employed as correction for multiple testing.
Genes up regulated in the dauer versus dauer-exit worms.
- WBPaper00038304:octr-1_regulated
Microarray data were subjected to the robust multichip averaging algorithm using GeneSpring GX software (Agilent Technologies, Santa Clara, CA). Analysis of variance t test and fold-change calculations were also performed using GeneSpring GX software. Probability calculations of enrichment were performed using the hypergeometric probability test (http://elegans.uky.edu/MA/progs/overlap_stats.html) to calculate the statistical significance of the overlap of gene groups.
Genes regulated by octr-1(ok371) after infected with P. aeruginosa PA14 for 4 hours at 25 centigrade.
- WBPaper00041207:PP_dauer_up
The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function. Control of FDR was employed as correction for multiple testing.
Pristionchus pacificus genes up regulated in the dauer versus dauer-exit worms.
- WBPaper00041207:PP_dauer_down
The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function. Control of FDR was employed as correction for multiple testing.
Pristionchus pacificus genes down regulated in the dauer versus dauer-exit worms.