Hi, I've recently started getting into using the beadarray package for reading Illumina microarray files, and am unfortunately asking questions already. I see that there is a background correction function for beadlevel data, but I can't find one yet for beadsummary data. Does beadsummary perform background correction automatically on the data, or should it be corrected within BeadStudio before exporting the files in the first place? thanks in advance, Gordon [[alternative HTML version deleted]]

Hi Gordon, There are two types of background correction used for Illumina data. The first is an image processing step and occurs at the bead-level (e.g. in the files such as where each bead is adjusted to adjust for local aberrations on the surface of the array. This is the backgroundCorrect function that you find in beadarray. The second occurs after summarisation, for example by the BeadStudio software, where each bead-type is adjusted for non-specific hybridisation using the values of negative controls on the same array. However, we find this type of correction introduces missing data and high variability so we don't usually recommend it. Background correction of summarized data isn't currently supported by beadarray. Mark On Tue, Jan 5, 2010 at 10:43 AM, <gblackshields at="" gmail.com=""> wrote: > Hi, > > I've recently started getting into using the beadarray package for reading > Illumina microarray files, and am unfortunately asking questions already. I > see that there is a background correction function for beadlevel data, but > I can't find one yet for beadsummary data. Does beadsummary perform > background correction automatically on the data, or should it be corrected > within BeadStudio before exporting the files in the first place? > > thanks in advance, > > Gordon > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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 >