[BioC] Microarray data annotation

[Sean Davis]

Ranga,

I think you already have the idea.  However, I have no idea why someone made
a big deal of the distinction to you.  Clearly, the only reason that
microarrays are useful is that they link expression levels of (somewhat)
known quantities to biological knowledge bases.  Usually, as you point out,
one knows the "identities" of the spots on a microarray (cDNA, oligo, BAC,
whatever) BEFORE one does the hybridization, so I can't think of a situation
where one has only raw data with NO annotation.  Even in the case of a truly
unknown EST, one still presumably has a sequence (or a way to retrieve it)
so that tools like BLAST, HMMER, etc. are available.  Therefore, I think
that the distinction here may be the way that the annotation is handled in
processing the raw data into useful biological information.  Sometimes, that
is quite straightforward, and sometimes it requires a devoted bioinformatics
team.

This is to be distinguished from retrieving the annotation and using it for
analysis.  Clearly, this is often another major bioinformatics feat (one
might argue that this is THE largest challenge in using microarray
technology right now) which BioConductor attempts to answer with the various
annotation packages.

Sean

On 6/29/04 9:10 PM, "Ranga Chari" <ranga_bioc at yahoo.com> wrote:

> Hello Group, 
> I am new to Microarray data analysis and statistics.  In microarray group
> circles people are talking about raw data, un-annotated raw data and annotated
> raw data. 
> Could any one please help me in explaining what exactly means annotated raw
> data. 
> Is this some thing to say that a particular spot gene name is "xxx" and it has
> some intensity levels xxx(ch1) xxxx (ch2) etc.
> If this is what is annotation component then the microarray raw data (cDNA)
> already has intensity levels linked to a gene and not some arbitarary code
> number. 
> 
> Could any one please post their understanding about annotated data.
> 
> thank you. 
> Ranga
> 
> 
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