I realized that there are many tools only support Affymetrix SNP array data analysis. Is there any way or is it reliable to convert illumina SNP array data to Affymetrixl-like format?
For example, HAPSEG and ABSOLUTE developed by Broad institute (http://www.broadinstitute.org/cancer/cga/absolute_run), which are tools to analyze tumor purity/ploidy, only support Affy SNP 6.0 and 250K array. Does that mean there's definitely no clue to analyze illumina SNP array data at hand? Would really appreciate any suggestions, thanks.