Visualizing SNP Data

Question

[jcn]

Hello all,

I have a SNP probes file that contains the headers "SNP ID," "Probe Name," "Chromosome," "SNP Position," "Feature Number," and "Genotype." My goal is to visualize this data, but a lot of the tools/packages I have been finding require information that I do not have. I have about ~40 of these files in a cohort, and my goal is to compare SNP data within the cohort. Any ideas as to what package to use to do this? The platform I am using is the Agilent system. I also have CGH data with the headers "Probe Name," "Chromosome," "start," "stop," Feature Number," "Log Ratio." If anyone knows how to use the SNP and CGH data together, please let me know!! Thanks all. :)

Best, C

[Mark]

Sounds like microarray data? Try R/bioconductor + limma package