[BioC] simpleaffy QCstats and affyQAReport repost

[Matt Settles]

My apologizes for the previous unintelligible post, apparently Windows
Live Mail does not allow for plain text emails.

to whom are interested,

I have two requests (with possible suggestions for updates). I use
affyQAreport for every dataset and I really like the results. It is
pretty complete and easy to understand, especially when your dealing
with a new biologist doing their first array experiment.

That being said
Issue #1
It would seem that I often get nonstandard affy arrays to work with.
I work with zebrafish, wheat, barley, bovine, as well as the typical
mouse, rat, and human.
In order to get zebrafish (and some rat) to work I need to edit the
simpleaffy ratio function. Apparently their qc probe names have a
non-standard format.
Also wheat, barley and bovine do not have the needed information for
qcstats to even run and crashes affyQAreport.

My fix so far
I've hacked the ratio function and the .qcenv so that my datasets will
work (also the hack does not seem to have effected any other array
types, so far anyway)
the code can be found at
http://mite.cswin.uidaho.edu/experiments/Rcode/modifiedQA.R
I source this file before running affyQAreport and all works.

It would seem pretty straight forward to not set up the .qcenv from
the data files at compile time but rather when the library loads, that
way someone could edit the data files to their needs. The files aren't
large so it doesn't seem like it would add any significant time to
loading the library.

Issue #2
I like underscores, I use them often in my filenames and I've found
them in some array probe names and of course latex requires you to
escape them and it complains (alot), but I can't do this within the
affyQAreport function.

My fix so far
the simple fix I use is to use the latex package underscore.sty.
So right now I edit each tex file to include
\usepackage{underscore}
and rerun pdflatex. I don't have write access to the R library folder
so I can't edit the latex template file.

If this would be an unobtrusive addition to the next update, it would
be greatly appreciated.

Matt Settles
PhD Candidate
Program in Bioinformatics and Compuational Biology
Department of Computer Science
Department of Biology
University of Idaho, Moscow, ID