geWorkbench

Page in preparation, should be available 11/22/2013.

Parameters

• Select Service
  • Local Service - run VIPER on an instance of R installed on the same machine as geWorkbench.
  • Web service - not yet implemented. Run Viper on a remote server.

• Select Regulon
  • hl60_cmap2_tf_regulon - Human promyelocytic leukemia, CMAP2 data
  • mcf7_cmap2_tf_regulon - Breast adenocarcinoma, CMAP2 data
  • pc3_cmap2_tf_regulon - Prostate cancer, CMAP2 data

• Select Method
  • none - use if the data is already in rank format.
  • scale - for each gene (row in dataset), calculate the mean and standard deviation across all columns, then subtract the mean from each value in the row, and divide each by the standard deviation.
  • rank - rank transform row-wise
  • mad - subtract the median, divide by the median absolute deviation (MAD)
  • ttest - for each gene, perform a t-test comparing each sample (column) one-at-a-time against all other samples taken together.