Hi everyone, Does anybody know a way to work with bead-level Illumina SNP data ? I'm interested in the correction of potential spatial bias on Illumina SNP arrays, especially the HumanCNV370-Quad beadChip. Usually people work with summarized data out from BeadStudio (either text files or idat files), but here I need to process the data in a different way : the correction on spatial bias must take place on the images of the array, i.e on bead-level data (.txt or .TIFF files). Hence I need to first apply my correction algorithm on the raw data, and then summarize the data to get the X and Y signal (one value per SNP) necessary to compute log R ratios and B allele frequencies. I found 2 packages to work on Illumina SNP data : beadarraySNP and crlmm. But we can only use idat files with these packages. So I use beadarray to handle the bead-level data files (I prefer to use the .txt files rather than the .TIFF images as the processing of .TIFF images takes time). But I'm still searching for a way to compute summarized data from bead-level data. I tried to reproduce the normalisation procedure described in the white paper ? Illumina's Genotyping Data Normalization Methods ? (cf. joined file), which details the procedure described in the founding article by Piffer et al. (ref : Peiffer, Gunderson et al., 2006, Genome Research). I believe this normalization procedure is the one implemented within BeadStudio. Here is the problem : appart from any normalization or correction of spatial bias, starting from bead-level data (either from .txt files or from TIFF images) I fail to obtain summarized values of X and Y (or R and Theta) identical or even close to X and Y values returned by BeadStudio for the same array. The data I get after a ? by hand ? normalization following the Illumina procedure is much more noisy and the signal to noise ratio is much lower, when compared to the output of beadStudio for the same array. Something go wrong but I can't identify what. If needed I can send a file with graphs show if the comparison. So here I need help : Does anybody know a way to work with bead-level Illumina SNP data ? How to normalize bead-level data, i.e compute the summarized X/Y (or R/theta) values from Illumina bead-level data ? Any help will be more than welcome. Best regards, Jonas -------------- next part -------------- A non-text attachment was scrubbed... Name: Illumina_NormalizationWhitePaper_revD_070820.pdf Type: application/pdf Size: 148631 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20100429="" 867c83bb="" attachment.pdf="">