Microarray Data Analysis Using BRB-ArrayTools Version 4.2.0 ...

Included plugins• Analysis of Variance – Up to four-way ANOVA. Options toinclude blocking factors or use random variance model.• ANOVA of log intensities – For dual-channel non-referencedesigns, model includes gene-specific array effect, dye effect,and class effect. Option to use random variance model.• ANOVA for Mixed Effects Model – Allows up to three fixedeffects and one random effect.• M vs A plot – For dual-channel data, plots log-ratio vs averagelog-intensity for all arrays.• Pairwise correlation – Plots heat map showing the matrix ofpairwise correlations among all arrays.• Smoothed CDF – Plots smoothed cumulative distributionfunction of log-red and log-green, or log-ratio for all arrays.• Export 1- and 2-color data to R – Exports data from ProjectWorkbook to files which can be imported into R.132