[BioC] Agilent 2-color Microarray data analysis tutorial

Yong Li yong.li at zbsa.uni-freiburg.de
Thu Jan 14 14:07:05 CET 2010

Dear Martin,

thanks for the useful links, especially the Bioconductor case studies 
book. I am also interested in the Agilent 2-color data analysis.

In the Bioconductor case studies book source code, the Chapter 4 Two 
Color Arrays is about the analysis of Agilent 2 color data processed 
with genepix image analysis program. I just have a question about 
filtering of such data. Normally filtering is done before finding 
differentially expressed genes (in this case with limma) and after 
normalization. Filtering out control probes is straightforward. What 
about other filtering criteria, such as IQR? How can filtering be 
applied to 2-color data in the form of RGlist or MAlist?


Martin Morgan wrote:
> Martin Morgan wrote:
>> Hi Chuming --
>> Chuming Chen wrote:
>>> Dear All,
>>> Can anybody point a tutorial on Agilent 2-color Microarray data analysis
>>> including pre-processing, statistical analyses, Gene set enrichment
>>> analysis, Clustering and visualization etc.?
>> The limma vignette is a very useful general purpose starting point,
>>   http://bioconductor.org/packages/2.5/bioc/html/limma.html
>> as are the workshop resources related to microarray analysis
>>   http://bioconductor.org/workshops/
>> and common workflows
>>   http://bioconductor.org/docs/workflows/index.html
> also the Bioconductor case studies book provides a very useful extended
> tutorial
>   http://bioconductor.org/pub/biocases/
>> Martin
>>> Thanks,
>>> Chuming
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