[BioC] about illumina data

Vincent Carey stvjc at channing.harvard.edu
Tue Sep 7 18:33:36 CEST 2010

Your questions are a little too broad to be answered comfortably,
likely the reason
for lack of response.  Comments below; please read the posting guide
before posting more.

On Sun, Sep 5, 2010 at 3:22 PM, zhliu.tju <zhliu.tju at gmail.com> wrote:
> Dear all,
> I am a rookie in microarray data analysis and I not familiar with illumina
> software and the result format of beadstudio software. Now I got microarray
> data, but I am not sure about the process they have done to these data.
> 1. Normalized data means they are preprocessed and normalized, if they are
> log transformed?

You are asking for a definition of "normalized"?  In general it means
there has been
an attempt to remove biologically unimportant sources of variation.
The bead studio documentation
should be consulted for details on what it can do, and the lab techs
should be queried
concerning what was actually done.

> 2. If I want to zscore transform the normalized data, if I should do log
> transformation first?

> 3. In addition, illumina microarray data is one channel data, but I donot
> know what is the difference between one channel data and two channel data?

You cannot reasonably expect readers of the the mailing list to
address this issue.  You have to do some reading
about general concepts of microarray analysis.  The table of contents
in the wikipedia article
http://en.wikipedia.org/wiki/Dna_microarray addresses the topic of one
vs two channels directly, and many other texts
can be found to introduce the concepts.

> Thanks a lot!
> Zhe
>        [[alternative HTML version deleted]]
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