Preprocessing Bioconductor Overview Data set Salmo, color flip design Name Cy5 Cy3 FileName array1 self1 self txt array2 self2 self txt RG$printer $ngrid.r [1] 12 $ngrid.c [1] 4 $nspot.r [1] 17 $nspot.c [1] 17 Red background Green background Plot raw data Raw data cartesian coordinates Raw data log scale Data background corrected MA plot before normalisation MA per print tip before normalisation MA after print tip normalisation Box plot Between array normalisation not essential SWIRL DATASET Between array normalisation essential Volcano plot Log oddsL Log(p/(1-p)) SALMO array 6 replicas (6 normalised ratios) Design > Salmo.cl Salmo.cl [1] SAM Paired, SAM CyberT Results CyberT Mn: mean ratio # obs: number of ratios available to calculate the statistics SD: standard deviation on the ratio estimates T, p calculated t and p value that indicate the significance of the measurement Results CyberT