Dear All, I have the following questions on arrayQuality: 1. The documentation for 9-mer hybridizations discusses gpr files (the output of GenePix). Can arrayQuality be used for output from Spot? 2. Is there a way to custom specify the location of the 9-mers? 3. A program called Acuity is cited. What is Acuity? 4. Several of the figures did not come out with the html file that was in the doc folder. Is a pdf file available? Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "If Dylan uses the word "the" and Donne uses the word "the" does he say that Dylan is making a reference to Donne?" -Rose Friedman, age 7

Dear Richard, We have been modifying several things in arrayQuality package since the release. The latest version of the package is available from our website http://arrays.ucsf.edu/software. In particular, the problem with the missing images in the manual should be fixed. You can install it by typing in R: install.packages("arrayQuality", contriburl="http://arrays.ucsf.edu/software") For Spot output: arrayQuality is not reading output from Spot directly at the moment. You can still generate diagnostic plots from a Spot file by reading your data into a RGList using the function read.maimage(source="spot") from limma, or into a marrayRaw object using read.Spot function from marray. Then, call the function maQualityPlots using your new object as argument. I am planning to extend the 9mers and QCHyb quality control functions to Spot files soon. "2. Is there a way to custom specify the location of the 9-mers?" I refer to 9-mers oligos as random small oligos that are hybridized to the array to verify that all spots have been printed properly, not to the actual probes on the arrays. As I am not sure to understand your question completely, could you please give me more details about what you would like to achieve? 3. Acuity Acuity is a software developed by Axon Instruments that we use as database, analysis and visualization tool. For more information: http://www.axon.com/gn_Acuity.html Regards, Agnes -----Original Message----- From: Richard Friedman [mailto:friedman@cancercenter.columbia.edu] Sent: Wednesday, July 07, 2004 12:16 PM To: 'Bioconductor Mail List' Subject: [BioC] Questions on arrayQuality Dear All, I have the following questions on arrayQuality: 1. The documentation for 9-mer hybridizations discusses gpr files (the output of GenePix). Can arrayQuality be used for output from Spot? 2. Is there a way to custom specify the location of the 9-mers? 3. A program called Acuity is cited. What is Acuity? 4. Several of the figures did not come out with the html file that was in the doc folder. Is a pdf file available? Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "If Dylan uses the word "the" and Donne uses the word "the" does he say that Dylan is making a reference to Donne?" -Rose Friedman, age 7 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor