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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.h tml#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="" covdes="" c.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.h tml#biocon_limmaaffy<http: faculty.ucr.edu="" %7etgirke="" documents="" r_bioc="" ond="" 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 > > > > -- > ?q???????r ?q???????r > {/ ???? /} {/ ???? /} > ( (oo) ) ( (oo) ) > ?????? ?????? > > ???q???r > /??????\ > ?? ?? > > -- > ?q???????r ?q???????r > {/ ???? /} {/ ???? /} > ( (oo) ) ( (oo) ) > ?????? ?????? > > ???q???r > /??????\ > ?? ?? -- 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