[BioC] data with known expressed genes

[Sean Davis]

On 4/24/06 3:46 PM, "Tony Zheng" <tonyzhe at gmail.com> wrote:

> Dear BioC Users:
> 
> I am looking for a data set with genes known to be differentially expressed
> in a two-treatment comparison, preferably with known genes ranking.

Most papers on a two-class comparison include a list of
differentially-expressed genes.  Much of the data used to produce such lists
is publicly available, but you will need to look in each paper to see if
that specific paper has publicly available data and where it is located.

> If I use the Affy HG_U133A data set, which cel files to be used for htis
> purpose and what are the gene ranking?

CEL files represent the data after image extraction and do not contain any
information about gene rankings, really.  There are several steps between
the generation of the CEL files by the image extraction software and
generating a gene ranking.  I would suggest getting a book or reading a
review article on microarray analysis.

I think I very well may have misunderstood what you were asking and I
certainly don't know what you want to do.  Perhaps rather than asking "how
do I do this specific thing" you could explain in more general terms what
you want to do.

Sean