Hi all, I have constructed cdf environment on my Mac. My environment and normalization by rma looks work under below working flow (******). But I can not get whole results. I got normalized data from each control gene spots but all spots data from genes has merged all in one line like "data ex.". copy9_.... means control spots. non_at and random_at means genes. I do not know why I can not get normalized data from all each spots. Could you please help me someone? "data ex." .....many control genes........... copy9_AFFX-r2-At-Ubq-5_s_at 10.8117692745457 10.9959999081142 10.1008637507680 10.0693470115082 copy9_AFFX-r2-At-Ubq-5_x_at 11.9637427616359 12.0014521293535 11.8231131697170 11.9823112800146 non_at 2.77632266000964 3.06545224338101 2.77787004643169 3.07748076274474 random_at 4.2258095000546 3.72907697958284 4.35455022393967 3.71650013156617 ****** > make.cdf.package("1-1.CDF", packagename="49chip14micronmercurycdf") Reading CDF file. Creating CDF environment Wait for about 6 dots....... Creating package in /Users/junshiyazaki/Desktop/R_test_data/49chip14micronmercurycdf [1] "49chip14micronmercurycdf" > cel.files=list.files(pattern=".CEL$") > data=ReadAffy(filenames=cel.files) > chip14micronmercurycdf=env > data@cdfName<- "chip14micronmercurycdf" > temp=rma(data) Background correcting Normalizing Calculating Expression > write.exprs(temp, file="mydata8.txt") ****** -- *********************************************************** *********************************************************** Junshi Yazaki, Ph D The Salk Institute for Biological Studies Plant Biology Laboratories 10010 North Torrey Pines Road La Jolla, CA 92037 Phone (858) 453-4100 x1533 FAX (858) 558-6379 Email: jyazaki@salk.edu Web addresses: http://signal.salk.edu http://qtlpc.salk.edu/pbio/Web/ecker.html