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Old 08-27-2015, 04:24 AM   #87
BobbyT
Junior Member
 
Location: Melbourne

Join Date: Aug 2015
Posts: 2
Default Missing samples on gage() > sigGeneSet() heatmap

Hello everyone. It's seems I'm a little late to this party. So fingers crossed this thread is still active.

So my problem is that only 3 of my 6 samples are appearing in heatmaps generated with sigGeneSet. The 'samp' samples are appearing but not 'ref' samples.

This only occurs when visualizing significant gene sets (gage() > sigGeneSet()). When running gage() > essGene() > geneData() to visualize genes in specific gene sets all samples are present (Figure 2, main vignette).

I have looked over the vignettes and sigGeneSet seem to always be pictured with 'samp' samples only (Figure 1, main vignette).

Is there a way to make sigGeneSet/gage generate heatmaps with all samples such as in Figure 2/3 of the main vignette but displaying gene set names as in Figure 1 of the main vignette?

Thanks,
BobbyT
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