[BioC] probeset for a single gene

[Henrik Bengtsson]

Hi.

On 11/11/06, Weiwei Shi <helprhelp at gmail.com> wrote:
> Hi,
> I went through the archive for a while and still did not find the good
> answer for that. Sorry for the re-post :(
>
> 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.

Are we talking about finding a function summarizing the probe
intensities in a probeset (as in Affymetrix arrays) to a single value?
 For 3' expression arrays there is plenty of algorithms/publications,
e.g. the single-chip model MAS 5.0, multi-chip models MBEI (dChip) and
RMA.  The following article lists many more with references:

Irizarry, R.A.; Wu, Z. & Jaffee, H.A. Comparison of Affymetrix
GeneChip expression measures. Bioinformatics, 2006, 22, 789-794

Best

Henrik


>
> 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?
>
> thanks
>
> --
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
>
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
>
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