How can I adapt the packages and algorithms for SNP calling Affymetrix chips for Fluidigm SNP chips? I am unfamiliar with Affymetrix chips and how they are normalized. The data that is exportable from the fluidigm chips comes out normalized already so I don't believe any normalization steps would be required. I would like a way to import the x and y data properly for each SNP and apply the existing algorithms for calling and be able to read up on what algorithm I'm using if it is successful. It would be important to have an algorithm that would be selective on calls and "no call" when appropriate. Thank you for your help. I've been searching and exploring different packages and options from publications but if someone could direct me to what they have found works well I would appreciate it greatly. To do the work of myself I believe I will need to know what packages are used to import the normalized data along with what functions are used and what functions are used for the genotyping algorithm. If I have these things I can manipulate my data to fit it. [[alternative HTML version deleted]]