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Allow for specification of multiple test datasets in the plotModule function. This would allow for plotting of average topology across datasets (i.e. mean coexpression, mean network edge weights, mean scaled connectivity). This would provide a more robust view of module topology, e.g. in the case where a module replicates in independent datasets.
Notes for implementation:
In this case, the default orderNodesBy should be set to the same argument as test. The 'data' and 'orderSamplesBy' arguments present a problem: the data cannot be averaged across independent datasets because the samples will not be the same. Calculating the mean topology across different data sources within the same samples (e.g. different tissues) is unlikely to be meaningful. Perhaps in this case, we would set the gene expression data and summary expression plots to show only the 'orderSamplesBy' dataset?
The text was updated successfully, but these errors were encountered:
Allow for specification of multiple
test
datasets in theplotModule
function. This would allow for plotting of average topology across datasets (i.e. mean coexpression, mean network edge weights, mean scaled connectivity). This would provide a more robust view of module topology, e.g. in the case where a module replicates in independent datasets.Notes for implementation:
In this case, the default
orderNodesBy
should be set to the same argument astest
. The 'data' and 'orderSamplesBy' arguments present a problem: the data cannot be averaged across independent datasets because the samples will not be the same. Calculating the mean topology across different data sources within the same samples (e.g. different tissues) is unlikely to be meaningful. Perhaps in this case, we would set the gene expression data and summary expression plots to show only the 'orderSamplesBy' dataset?The text was updated successfully, but these errors were encountered: