[BioC] cDNA raw data

[Srinivas Iyyer]

Hello all,
  pardon me for asking a simple question.  in an affy
experiment where one sample per one chip is used, it
is very clear for me that an affy cel file is derived
from one sample.  So in the raw data I have, an affy
study has 20 normal samples, 40 prostate cancer and
final 40 neoplastic prostate tissues. So a total of
100 affy cel files (from 100 chips, 100 samples) are
made. 

In a cDNA experiment, from the raw data, it is very
difficult for me to identify which samples is used for
cy3 and which sample is used for cy5. How can I have
intensity for a cy3 tagged sample and cy5 tagged
sample.

For example in the link given below:
http://llmpp.nih.gov/lymphoma/data/rawdata/

Lymphoma chip is used. It is my understanding that all
cDNAs know to be part of lymphoma are printed on this
chip.  Here the first sample is  mentioned as lc8n076
as Blood B cells.  When I click the data link I see
Ch1  mean Ch2 mean, ch1 median and ch2 median values. 
In this case how do I know why sample is reference
sample tagged with cy3 and which sample is tagged with
cy5. 

I am asking a simple question, and sincerly I do not
know to the answer and I am seeking help of scientists
who have a lot of experience to help me in
understnding this concept. I really appreaciate your
help. 

Thank you. 

Srini Iyyer