[BioC] About Analysis of Differentially Expressed Genes in R & BioConductor Manual

[Thomas Girke]

Dear Alex,

Please consult the limma and simple affy manuals if these steps are
unclear to you. The provided online course material is just a command summary that
introduces a series of BioC packages. It is not intended as a substitute 
for the main manuals of these packages. 

Thomas


On Wed 06/27/07 21:08, ssls sddd wrote:
> Hello! This message is especially for Dr.Thomas Girke.
> I am following the codes presented in
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#BioCprimer<http://faculty.ucr.edu/%7Etgirke/Documents/R_BioCond/R_BioCondManual.html#BioCprimer>
> to analyze the gene expression data.
> 
> A zipfile with 6 .cel files was provided and I instead used 6 of my own
> arrays for test.
> I had no problem in "Generate RMA expression data, MAS5 P/M/A calls and
> export results to Excel". I skipped "Add annotation information" because I
> don't know which
> annotation file is for my arrays. I did "Visualization and quality control".
> I decided to do "Simple Affy" and "Identify differtially expressed genes
> (DEGs) with the limma package".
> 
> But the 1st question is that, for "Simple Affy", I have no idea how to make
> the "covdesc.txt" file,
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/Samples/covdesc.txt
> <http://faculty.ucr.edu/%7Etgirke/Documents/R_BioCond/Samples/covdesc.txt>
> 
> the 2nd question is that, for "Identify differtially expressed genes (DEGs)
> with the limma package", which leads to the session of "Limma Section for
> Affy Data",
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#biocon_limmaaffy<http://faculty.ucr.edu/%7Etgirke/Documents/R_BioCond/R_BioCondManual.html#biocon_limmaaffy>
> .
> 
> This requires a file called "affy_targets.txt",
> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/affy_targets.txt<http://faculty.ucr.edu/%7Etgirke/Documents/R_BioCond/affy_targets.txt>.
> 
> I also have no idea about how to make this one.
> 
> If you have any suggestions, please let me know. I really appreciate!
> 
> Thanks!
> 
> Alex
> 
> 
> 
> -- 
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-- 
Thomas Girke
Assistant Professor of Bioinformatics
Director, IIGB Bioinformatic Facility
Center for Plant Cell Biology (CEPCEB)
Institute for Integrative Genome Biology (IIGB)
Department of Botany and Plant Sciences
1008 Noel T. Keen Hall
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Website: http://faculty.ucr.edu/~tgirke
Ph: 951-827-2469
Fax: 951-827-4437