Posted on Friday, October 26, 2012 at 01:49PM by David Eby
Welcome to the GenePattern blog! We are launching this as a place where we can post important news and announcements for the GenePattern community with more detail than can fit into a system announcement or tweet. Feel free to give us feedback and ask questions using the Comments section below.
Posted on Sunday, September 30, 2012 at 12:32PM by The GenePattern Team
In GenePattern, you use the ComparativeMarkerSelection module to identify the genes (if any) that are differentially expressed between two phenotype classes. Typically, this is a three-step process:
Posted on Saturday, September 15, 2012 at 12:29PM by The GenePattern Team
In cancer genomics, copy number change is one of the hallmarks of the genetic instability common to most human cancers and loss of heterozygosity (LOH) of tumor suppressor genes is a crucial step in the development of sporadic and hereditary cancer (Monti, 2005). Using modules available in GenePattern, you can compute SNP copy number and LOH based on Affymetrix SNP chip data for paired target/normal samples and then view them in the Integrative Genomics Viewer (IGV). The following modules are used for this computation, with IGV at the end for viewing the results:
SNPFileCreator converts the .CEL files from an Affymetrix array into a GenePattern .SNP file. Raw data for the probes in each SNP probe set are converted to a single intensity value per SNP using one of four modeling algorithms: Average Difference, PM/MM Difference Model (dChip, the default), Median Probe, or Trimmed Mean....