[BioC] probeset for a single gene

[Sean Davis]

On Friday 10 November 2006 13:01, Weiwei Shi wrote:

> suppose i have some probes for the same gene, I am wondering which is
> the proper way to get a statistic for the expression for this gene?
> using mean, median or max or min? I think it might be affected by the
> research target but I wondering if there is some ref on it.

Hi, Weiwei.

There is not a standard, no.  The answer does probably depend on the research 
question (as you suggest), the type of data, quality metrics, and probably 
other factors.  Some of those "other factors", such as cross-hybridization, 
are not readily available in every case without some additional work.  

> btw, is there some ref on the data pre-processing (gene selection,
> multiple comparison, better with case study) for microarray analysis
> other than bioconductor book?

The microarray literature is relatively large, but there are many papers on 
all of the aspects that you mention above.  A good place to start if you have 
the bioconductor book is with the references therein.

Sean