Hello everyone, I would like to first to thank you all for providing such a great service. I've download the code base and played around with it, but I have a couple of straightforward questions. I am trying to load my own data but I am unsure as to what format(s) I should place it in. I have 2-colored cDNA and I have seen the swirl data you have provided but I am not certain if I have to map my data to that format. Here at George Mason University, we use QuantArray so our data comes out with the following format: >Number Array Row Array Column Row Column Name X Location Y >Location ch1 Intensity ch1 Background ch1 Intensity Std Dev ch1 >Background Std Dev ch1 Diameter ch1 Area ch1 Footprint ch1 >Circularity ch1 Spot Uniformity ch1 Bkg. Uniformity ch1 Signal Noise >Ratio ch1 Confidence ch2 Intensity ch2 Background ch2 Intensity Std >Dev ch2 Background Std Dev ch2 Diameter ch2 Area ch2 Footprint >ch2 Circularity ch2 Spot Uniformity ch2 Bkg. Uniformity ch2 Signal >Noise Ratio ch2 Confidence Ignore Filter My second question is I would like to have the classes you have created read directly from my database if possible. Do you have any suggestions as to how that can be approached? Sincerely, Ali Al-Timimi Graduate Student Center for Biomedical Genomics and Informatics George Mason University

Hi Ali, with regards to reading data from QuantArray, you can always use the R functions read.table or read.delim (type "help(read.delim)" at the R prompt) and then later call the constructors e.g. for marrayRaw with the appropriate matrices. However, Sandrine Dudoit would know much better about this! >My second question is I would like to have the classes you have created read >directly from my database if possible. Do you have any suggestions as to how >that can be approached? Check out the DBI: R/Splus Database Interface at http://cran.r-project.org/ -> Package Sources. or the various DBMS-specific packages. Best regards Wolfgang Dr. Wolfgang Huber http://www.dkfz.de/abt0840/whuber Tel +49-6221-424709 Fax +49-6221-42524709 DKFZ Division of Molecular Genome Analysis 69120 Heidelberg Germany -----Original Message----- From: bioconductor-admin@stat.math.ethz.ch [mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of Ali Al- Timimi Sent: Monday, September 30, 2002 9:53 PM To: bioconductor@stat.math.ethz.ch Subject: [BioC] A couple of questions Hello everyone, I would like to first to thank you all for providing such a great service. I've download the code base and played around with it, but I have a couple of straightforward questions. I am trying to load my own data but I am unsure as to what format(s) I should place it in. I have 2-colored cDNA and I have seen the swirl data you have provided but I am not certain if I have to map my data to that format. Here at George Mason University, we use QuantArray so our data comes out with the following format: >Number Array Row Array Column Row Column Name X Location Y >Location ch1 Intensity ch1 Background ch1 Intensity Std Dev ch1 >Background Std Dev ch1 Diameter ch1 Area ch1 Footprint ch1 >Circularity ch1 Spot Uniformity ch1 Bkg. Uniformity ch1 Signal Noise >Ratio ch1 Confidence ch2 Intensity ch2 Background ch2 Intensity Std >Dev ch2 Background Std Dev ch2 Diameter ch2 Area ch2 Footprint >ch2 Circularity ch2 Spot Uniformity ch2 Bkg. Uniformity ch2 Signal >Noise Ratio ch2 Confidence Ignore Filter My second question is I would like to have the classes you have created read directly from my database if possible. Do you have any suggestions as to how that can be approached? Sincerely, Ali Al-Timimi Graduate Student Center for Biomedical Genomics and Informatics George Mason University _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor