SI Text R –based script for the analysis of whole genome (8x15.docVIP

SI Text R –based script for the analysis of whole genome (8x15K) microarrays comparing a DDT resistant field population with two more susceptible West African colonies, Akron (Benin) and Ngoussou (Cameroon). ############################################################################LIMMA NORMALISATION OF RAW DATA - DDT 8x15k MICROARRAYS (three way # # comparison, looped design) # ########################################################################### #Create a number of files for this process: ##Target file – listing the following for each array #FileName Treatment GErep cy3 cy5 date arraynumber slide ##Spot Type file – containing info on each spot type and designating a #colour to the spot types for subsequent plots i.e. #SpotType ControlType ProbeName GeneName colour #detoxtarget 0 DETOX_* * brown #WGtarget 0 CUST_* * black #CV 0 CV_A_90_P* * yellow #Brightcorner 1 GE_BrightCorner * orange #Darkcorner 1 DarkCorner * grey #positivecontrol 1 * * green #negativecontrol -1 * NegativeControl red ##Design file – containing a row for every sample on all arrays; must be in #the same order the arrays will be combined in at a later step i.e. array #numbers and cy3(Green) cy5(Red) order. #Array Dye Sample Group #U252705710011_S01re-b_GE2_105_Jan09_2_2.txt Cy5 1 ddt #U252705710011_S01re-b_GE2_105_Jan09_2_2.txt Cy3 4 akron #U252705710007_S01re-b_GE2_105_Jan09_1_2.txt Cy5 4 akron #U252705710007_S01re-b_GE2_105_Jan09_1_2.txt Cy3 8 ngou #U252705710007_S01re-b_GE2_105_Jan09_2_4.txt Cy5 8 ngou #U252705710007_S01re-b_GE2_105_Jan09_2_4.txt Cy3 2 ddt #U252705710011_S01re-b_GE2_105_Jan09_1_3.txt Cy5 2 ddt #U252705710011_S01re-b_GE2_105_Jan09_1_3.txt Cy3 6 akron #set working directory – in R using LIMMA MAANOVA setwd (c:/Documents and Settings/LOCATION OF SCAN FILES) getwd() #open limma source(