FLAME: View published data
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:
- Login to the public GenePattern server: http://genepattern.broadinstitute.org/gp/.
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).
- Click Run.
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
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Samples
The following table lists the samples in the T cell phosphorylation dataset analyzed in Pyne et al. (2009). The parameters used for the analysis are available at ftp://ftp.broadinstitute.org/pub/genepattern/example_files/FLAME/phospho.lymphgated.pipeline.parameters.txt. Use the previous procedure to display analysis results for a selected sample.
