hello folks, i am learning R and microarray analysis from scratch using different sites. today i am doing an exercise from http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#R_functions the section i am at is 2. Affymetrix data analysis. I understand the syntax given in this section up until: design <- model.matrix(~ -1+factor(c(1,1,2,2,3,3))) # Creates appropriate design matrix. Alternatively, such a design matrix can be created in any spreadsheet program and then imported into R. i am stuck at this point. i believe the model.matrix is creating a design matrix that the data will be put in later. the data in the example is: Name FileName Target Shoot12h.1 COLD_CONTROL_12H_SHOOT_REP1.cel c12h Shoot12h.2 COLD_CONTROL_12H_SHOOT_REP2.cel c12h ColdShoot6h.1 COLD_6H_SHOOT_REP1.cel t6h ColdShoot6h.2 COLD_6H_SHOOT_REP2.cel t6h ColdShoot12h.1 COLD_12H_SHOOT_REP1.cel t12h ColdShoot12h.2 COLD_12H_SHOOT_REP2.cel t12h Three experimental samples (duplicates of each giving a total of 6 arrays). now back to where i got stuck: design <- model.matrix(~ -1+factor(c(1,1,2,2,3,3))) # Creates appropriate design matrix. Alternatively, such a design matrix can be created in any spreadsheet program and then imported into R. what is model.matrix exactly doing? my real data that i will analyze after figuring this out has 49 arrays (columns): 3, 6, 9, 12 month samples with 9 replicates each and then 23 month samples with 13 replicates == total 49. how should i create an appropriate design matrix?? PLEASE help? thanks, daniel -- View this message in context: http://r.789695.n4.nabble.com/PLEASE-HELP-creating-a-matrix-tp4340263p4340263.html Sent from the R help mailing list archive at Nabble.com.