[BioC] cDNA raw data

Sean Davis sdavis2 at mail.nih.gov
Thu Dec 23 14:29:14 CET 2004

In short, one has to be "told" by the experimenter.  There is not a 
standard (nor should there be) for hybridization.  However, for storing 
and reporting data, there IS a standard which is followed less often 
than it should be.


On Dec 23, 2004, at 12:49 AM, Srinivas Iyyer wrote:

> 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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