Question: simpleaffy QCstats and affyQAReport repost
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gravatar for Matt Settles
11.8 years ago by
Matt Settles70
United States
Matt Settles70 wrote:
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
zebrafish probe affy • 435 views
ADD COMMENTlink modified 11.8 years ago by Crispin Miller1.1k • written 11.8 years ago by Matt Settles70
Answer: simpleaffy QCstats and affyQAReport repost
0
gravatar for Crispin Miller
11.8 years ago by
Crispin Miller1.1k
Crispin Miller1.1k wrote:
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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
ADD COMMENTlink written 11.8 years ago by Crispin Miller1.1k
Dear All, I've added three functions to the devl version of simpleaffy (2.11.22). These allow you to add (or change) the QC parameters for a chip if it's not in simpleaffy. These are: setAlpha(...) setAllSpikeProbes(...) and setAllQCProbes(...) For example: > cdfname <- cleancdfname(cdfName(eset)) > setAlpha(cdfname,0.05,0.065) Will add alpha1 and alpha2 values for the arraytype specified by cdfname (in this case taken from an ExpressionSet object). Similarly, setAllSpikeProbes() needs the probeset names for the four BioB, BioC, BioD and CreX spikes, and setAllQCProbes(...) needs the 3',M and 5' probesets for gapdh and beta-actin. Thus: setAlpha("hgu133plus2cdf",0.05,0.065) setAllQCProbes("hgu133plus2cdf", "AFFX-HSAC07/X00351_3_at","AFFX-HSAC07/X00351_M_at","AFFX- HSAC07/X00351_ 5_at", "AFFX-HUMGAPDH/M33197_3_at","AFFX- HUMGAPDH/M33197_M_at", "AFFX-HUMGAPDH/M33197_5_at") setAllSpikeProbes("hgu133plus2cdf", "AFFX-r2-Ec-bioB-3_at", "AFFX-r2-Ec-bioC-3_at", "AFFX-r2-Ec-bioD-3_at","AFFX-r2-P1-cre-3_at") Would (if you needed to) set up the hgu133plus2 array. Crispin -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}
ADD REPLYlink written 11.8 years ago by Crispin Miller1.1k
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