Hi Hao, There are probably better ways to do this, but here is how I have done it in the past. tmp <- pData(A) ## this will give you the existing phenoData object Now, tmp is a data.frame, and you will most likely want to have everything you add be a factor. Here is an example using some random cel files: >dat <- ReadAffy() > tmp <- pData(dat) > tmp sample 12_13_02_U133A_Mer_Latin_Square_Expt1_R1.CEL 1 12_13_02_U133A_Mer_Latin_Square_Expt1_R2.CEL 2 12_13_02_U133A_Mer_Latin_Square_Expt1_R3.CEL 3 12_13_02_U133A_Mer_Latin_Square_Expt10_R1.CEL 4 12_13_02_U133A_Mer_Latin_Square_Expt10_R2.CEL 5 12_13_02_U133A_Mer_Latin_Square_Expt10_R3.CEL 6 12_13_02_U133A_Mer_Latin_Square_Expt11_R1.CEL 7 12_13_02_U133A_Mer_Latin_Square_Expt11_R2.CEL 8 12_13_02_U133A_Mer_Latin_Square_Expt11_R3.CEL 9 12_13_02_U133A_Mer_Latin_Square_Expt12_R1.CEL 10 This is what you get if you never put in any phenoData in the first place. Now, if I used two different scanners, I could add a column like this: >tmp <- cbind(tmp, scanner = factor(c(1,1,1,1,1,2,2,2,2,2))) > tmp sample scanner 12_13_02_U133A_Mer_Latin_Square_Expt1_R1.CEL 1 1 12_13_02_U133A_Mer_Latin_Square_Expt1_R2.CEL 2 1 12_13_02_U133A_Mer_Latin_Square_Expt1_R3.CEL 3 1 12_13_02_U133A_Mer_Latin_Square_Expt10_R1.CEL 4 1 12_13_02_U133A_Mer_Latin_Square_Expt10_R2.CEL 5 1 12_13_02_U133A_Mer_Latin_Square_Expt10_R3.CEL 6 2 12_13_02_U133A_Mer_Latin_Square_Expt11_R1.CEL 7 2 12_13_02_U133A_Mer_Latin_Square_Expt11_R2.CEL 8 2 12_13_02_U133A_Mer_Latin_Square_Expt11_R3.CEL 9 2 12_13_02_U133A_Mer_Latin_Square_Expt12_R1.CEL 10 2 Once you have the phenoData set up the way you like, you can put it back like this: pData(A) <- tmp As for a good tutorial, you might look at End2End by Rafael Irizarry and Robert Gentleman. It gives a step-by-step tutorial that is quite nice. http://www.bioconductor.org/labMat/pdf/End2EndLab.pdf HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Hao Liu <liuha@umdnj.edu> 02/03/04 12:39PM >>> Dear All: I used AffyBatch(), and made an AffyBatch object named A by getting all the CEL files in the directory (which has about 150 cel files). However, I wonder if I can add pheno object to this object after its creation. And, if possible, where can I get some good tutorials on using Affy? Most materials I found are hard to understand, I need some step by step or examples. I am new in R and Bioconductor, please help. Thanks Hao Liu, Ph. D _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor