Hi Weili You can check the "methylumi" package for the methylation data input file format information, and the developing version of "lumi" package for the preprocessing of Infinium 450K methylation data. Pan Date: Thu, 21 Jul 2011 11:54:52 +0800 From: weili yan <01.weili@gmail.com> To: <bioconductor@stat.math.ethz.ch> Subject: [BioC] how to get the LIMMA required files for analysis from Illumina Methylation450K chip assay Message-ID: <caeqrnaftel-o1+qa7ozoxol+2esc_qfzggj- amky70lz9oui0q@mail.gmail.com=""> Content-Type: text/plain Dear Sir, We performed a genomewide methylation assay among a 6:6 case-control sample. It is a two-colour signal data. We got 4 data files after the data analysis by using Illumia GenomeStudio-Methylation software. My question is how can I extract data files required by LIMMA? I hope to genotype the differential loci indicated by the discovery array in a larger sample, and perform association analysis between methylation status or degree with quantitative or qualitative phenotypes. LIMMA is no doubt the right tooll to do this. However, we got problems in transfering Illumia data files to LIMMA. Do you have any training or online learning materials about this? How can I get help from you? Best wishes Weili -- WeiliYan, PhD, Director Department of Clinical Epidemiology Children's Hospital of Fudan University 399 Wanyuan Road Minhang District, Shanghai 201102 Tel&Fax: (86) 21 64931215 [[alternative HTML version deleted]] [[alternative HTML version deleted]]