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 they are pretty complete and easy to understand, especially when your dealing with a new biologist doing their first array experiment. That being saidIssue #1It would seem that I get some nonstandard affy arrays to work with.I work with zebrafish, wheat, barley, bovine, as well as the typical mouse, rat, and humanIn 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 fixI've hacked the ratio function and the .qcenv so that my datasets will work (also the hack has not effected any other arrays, so far anyway)the code can be found athttp://mite.cswin.uidaho.edu/experiments/Rcode/modifiedQA.RI source this file before running affyQAreport and all worksIt 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 #2I like underscores, I use them often in my filenames and of course latex requires you to escape them and it complains (alot), but I can't do this within affyQAreport.My fixthe simple fix I use is to use the latex package underscore.stySo right now I need to add the underscore style file to the affyQAreport output directory, edit the 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 fileIf this would be an unobtrusive addition to the next update, it would be greatly appreciated.Matt SettlesPhD CandidateProgram in Bioinformatics and Compuational BiologyDepartment of Computer ScienceDepartment of BiologyUniversity of Idaho, Moscow, ID
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