[BioC] Affy normalized data using cdf env and rma

[Junshi Yazaki]

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 at cdfName<- "chip14micronmercurycdf"
>  temp=rma(data)
Background correcting
Normalizing
Calculating Expression
>  write.exprs(temp, file="mydata8.txt")
******
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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 at salk.edu
Web addresses:
http://signal.salk.edu
http://qtlpc.salk.edu/pbio/Web/ecker.html