Thanks, I think I am getting there, one more question. I got the default phenodata using > defaultpheno <- pData(myAffyBatch); I know I can read a data frame and assign it as pData for my AffyBatch. I noticed that in my defaultpheno, the first column are as A.CEL B.CEL etc......... in my read in file, however, first line is like: A B etc... the questions, do I have to make the first column the same as the default one? I suspect I probably have to do so since otherwise, I am afraid the linkage will be severred. Thank you all for your kind reply Best Hao On Tue, 3 Feb 2004, Rafael A. Irizarry wrote: > yes you can. > > first creat a phenodata object using read.phenoData (read the help file > for more info), for example, > > pd <- read.phenoData(filename="pheno.txt") > > and then simply type > > phenoData(abatch) <- pd > > -r > > here is an example of a pheno.txt file: > > label otherstuff RNA > Empty 0 0 0 > NoRNA 1 1 0 > NotLabeled 0 1 1 > BA_polyGRNA 1 1 1 > > > On Tue, 3 Feb 2004, Hao Liu wrote: > > > 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 > > > Best regards Hao Liu, Ph. D

I tried to use exprs to get expset by > exp <- exprs(myAffyBatch) I then tried to write: exprs.write(exp,file=**,sep=*) however, I can't do this, seems exp is not really a expset object. Best regards Hao Liu, Ph. D