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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