What format(s) of experiment data can I upload into PS6 for analysis?

You can upload tab-delimited files, MS Excel files, Affymetrix .cel files or .chp files and GEO dataset SOFT files using the importer.

When importing tab-delimited or MS Excel files the data can be sample data (such as ID and intensity or other measured values) or can be data already analyzed (such as fold-change and p-values).  If you upload sample values, Pathway Studio can provides the ability to 1) view the sample data through a Correlation Viewer to identify potential outliers, 2) add annotation to individual samples, 3) set up multiple user-defined comparisons between sample groups (based on user provided annotation) and 4) compute ratio/fold-change values and p-values for the comparisons.  If the imported data contains already computed results of the analysis, the user can simply skip through steps 1-4 listed above and import the tables of results for viewing and further pathway analysis in Pathway Studio utilizing such tools at Gene Set Enrichment Analysis and Sub-Network enrichment analysis.  In addition, PS Enterprise provides the Build Dense Expressed Networks analysis tool.