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/ - 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? - 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? 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.

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.