[BioC] cDNA raw data

[michael watson (IAH-C)]

Hi

At the top of one of the data files I opened is:

REMARK	CH1 IMAGE	lc8n076_532 nm
REMARK	CH2 IMAGE	lc8n076_635 nm

Now the numbers 532 and 635 stand out (because I know about these things) - 532 is the scanning frequency of Cy3, and 635 the scanning frequency of 635.  So for this data set, Ch1 is Cy3 and Ch2 Cy5.

It may change for each data set though!  (and this is why data shoule be released in a MIAME compliant format....) :-)

Mick


-----Original Message-----
From:	bioconductor-bounces at stat.math.ethz.ch on behalf of Srinivas Iyyer
Sent:	Thu 12/23/2004 5:49 AM
To:	bioconductor at stat.math.ethz.ch
Cc:	
Subject:	[BioC] cDNA raw data
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

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