[BioC] Beginner: resources, WebArray and CARMAweb.

[James W. MacDonald]

Hi Paolo,

Paolo Innocenti wrote:
> Hi all,
> I'm a new PhD student: I will work on gene expression in Drosophila 
> (using Affymetrix GeneChip 2.0), but before running the arrays I would 
> like to learn how to analyze them.
> After successfully installing R and the BioConductor packages, I have 
> some problems in finding the right packages for my purposes.
> 
> My questions:
> 
> - A good place to begin with? I found these links:
> 	http://www.bioconductor.org/docs/
> 	http://www.bioconductor.org/pub/docs/mogr/

Both excellent resources. You might also look at the BiocViews page, 
which breaks down the packages based on what they are used for:

http://www.bioconductor.org/packages/2.0/BiocViews.html

> 
> - Where can I find raw data (the concept of raw data is still unclear in 
> my mind) in the right format (the concept of right format is still 
> unclear as well) to improve my skills in R and to test the packages?

You can get raw data from GEO. Not all entries have raw data, but many 
do. In this case raw data means celfiles (files with a .CEL subscript), 
which are what you get from the Affy scanner. I haven't used the GEO 
website extensively, but I believe you can search for things there which 
might help you narrow your focus.

You can also download data directly into R using the GEOquery package, 
but that presupposes you know what data you want to get.


> 
> - I found a few web-based applications for "friendly" microarray 
> data-analysis, using R and BioConductor packages (e.g. WebArray or 
> CARMAweb): are they a good substitute for the command-line (at least 
> during the apprenticeship), widespread-used?

You would have to talk to the WebArray or CARMAweb folks to know how 
widespread their use is. There are some GUI packages like affylmGUI that 
may be of some help to you as well.

Best,

Jim


> 
> Thanks,
> kind regards,
> Paolo Innocenti
> 
> PS. More details: I work on sex-dependent gene expression in D. 
> melanogaster, looking for sexual conflict in different loci, so I will 
> (roughly) make a comparison between expression of genes in high- and 
> low-fitness male, high- and low-fitness female, and the offspring.
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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