[BioC] simpleaffy QCstats and affyQAReport repost

[Crispin Miller]

Hi Matt,
You are right - the qc bits of simpleaffy are rather brittle if they
encounter an array they don't know about - I'm working on something to
make it more graceful (and easier to deal with than having to hack the
internal functions ;-))
I'll keep you posted.
best,

Crispin
 

> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch 
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of 
> Matt Settles
> Sent: 04 August 2007 02:46
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] simpleaffy QCstats and affyQAReport repost
> 
> 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
> 
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