Pyne et al. (2009) present three datasets in their manuscript. Analysis results for the T cell phosphorylation data are available on the GenePattern ftp site. To view the clusters identified by FLAME for a given sample in this published data, use the FLAMEContourViewer.Pipeline. The pipeline first runs the FLAMEContourDataGenerator module to generate the data required to display a 3-D contour plot of the clusters in a given sample. It then opens the FLAMEViewer to display a 3-D scatterplot and 3-D contour plot of the clusters in the sample.
To run the pipeline for a given sample from the published data:
If you do not have a GenePattern account, you can register on the login page.
Result: GenePattern displays its main page.
Click a sample name in the table below.
The table lists each sample in the T cell phosphorylation dataset.
Result: GenePattern displays the FLAMEContourViewer.Pipeline page. It automatically populates the parameter fields with the result files for the selected sample.
Optionally, modify the channels to plot parameter.
Pyne et al. (2009) clustered four channels: SLP76,ZAP70,CD4,CD45RA. The FLAMEViewer uses three channels to display a 3-D contour plot of the clusters in the sample. Select the three channels to use (default: SLP76,ZAP70,CD4).
Result: GenePattern runs the FLAMEContourDataGenerator to generate data for the 3-D contour plot. It then opens the FLAMEViewer to display both a 3-D scatterplot and 3-D contour plot of the clusters in the sample. For instructions on how to use the viewer, see the FLAMEViewer documentation .