Hello, I am a novice in this area, and I apologize before hand for my ignorance !I have a question related to the Bead Array package. My understanding is that Bead Array can do the genotyping calls and generate something comparable to the Final Report using BeadStudio. Is that correct ? Further, I am able to read in the Bead Level data, and do things as described in the vignette for Analysis of Bead Level Data. But one thing I can't figure out is how the genotyping is done. Since no reference is made about this in the vignette or related literature, makes me to believe that there is something that I am totally missing or that the genotyping is intuitive and unfortunatley I don't know how that is done . I hope someone can clarify these questions. Any help will be most appreciated. Thanks, Divinya

Dear Divinya, At present there is no functionality in the beadarray package to produce genotype calls from the raw data. I know that Rafa and Benilton are in the process of modifying the genotyping routines in the oligo package to handle Illumina data, but I'm not sure how far advanced this is and whether it uses the raw data as its starting point. Best wishes, Matt > Hello, > I am a novice in this area, and I apologize before hand for my ignorance !I > have a question related to the Bead Array package. My understanding is that > Bead Array can do the genotyping calls and generate something comparable to > the Final Report using BeadStudio. Is that correct ? > Further, I am able to read in the Bead Level data, and do things as > described in the vignette for Analysis of Bead Level Data. But one thing I > can't figure out is how the genotyping is done. Since no reference is made > about this in the vignette or related literature, makes me to believe that > there is something that I am totally missing or that the genotyping is > intuitive and unfortunatley I don't know how that is done . > I hope someone can clarify these questions. Any help will be most > appreciated. > > Thanks, > Divinya