Drear All, Is it appropriate to apply the "rma" background adjustment to the Nimblegen arrays? Can it be done by hacking the rma code? The background is the background intensity around the features or is it the non-specific binding? As I understand it, the features on the Nimblegen arrays are next to each other (no gaps). In addition, it has probably been asked many times. What is the background correction method for the rma algorithm (in simple terms)? Thanks for your expert advice. Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside Boulevard Woodbury, NY 11797 (516)422-4076

not hack is needed if you're using the oligo package... you'd need: - XYS files provided by NimbleGen - a data package specific to the array you're working with (built via makePlatformDesign) Then, library(oligo) x=read.xysfiles(list.xysfiles()) y=rma(x) The following might be useful: http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalho/ tutorial-slides.pdf Please, let me know if you need more help (the packages are not documented yet, but i'm working on this). b On Feb 28, 2007, at 12:31 PM, Khan, Sohail wrote: > Drear All, > > Is it appropriate to apply the "rma" background adjustment to the > Nimblegen arrays? Can it be done by hacking the rma code? The > background is the background intensity around the features or is it > the non-specific binding? As I understand it, the features on the > Nimblegen arrays are next to each other (no gaps). In addition, it > has probably been asked many times. What is the background > correction method for the rma algorithm (in simple terms)? > Thanks for your expert advice. > > > Sohail Khan > Scientific Programmer > COLD SPRING HARBOR LABORATORY > Genome Research Center > 500 Sunnyside Boulevard > Woodbury, NY 11797 > (516)422-4076 > > _______________________________________________ > 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

Khan, Sohail wrote: > Drear All, > > Is it appropriate to apply the "rma" background adjustment to the Nimblegen arrays? I should hope so - we apply it to all of the expression data that we process and ship to customers. :) > Can it be done by hacking the rma code? As Benilton pointed out, the easiest way to use rma on your expression data (if you are not a service customer) is to use the oligo package. The background is the background intensity around the features or is it the non-specific binding? As I understand it, the features on the Nimblegen arrays are next to each other (no gaps). In addition, it has probably been asked many times. What is the background correction method for the rma algorithm (in simple terms)? > Thanks for your expert advice. > The background in this case is the non-specific binding, not an image-based background correction. The experimental features on most NimbleGen arrays are arranged in checkboard fashion, meaning that there is an empty feature on all four sides of every experimental feature. However given the size of the features (16 microns) and a standard 5 micron scanner, features are only 3x3 pixels. Since there is some amount of signal bleed-over you would want to ignore a 1 pixel border in the empty features, leaving you with 4 pixels of background information that you would want to use. With a higher resolution scanner, you have more pixels to play with, and image-based background correction is probably more feasible. Todd -- Todd Richmond, PhD Manager of Research Informatics NimbleGen Systems, Inc Madison, WI 53719 1-608-218-7600