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markziemann / mitch

An R package for multi-dimensional pathway enrichment analysis
https://bioconductor.org/packages/mitch
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Error in sparse matrix #16

Closed markziemann closed 4 years ago

markziemann commented 4 years ago

With the detailed gene set reports in both the mitch_plots and mitch_report I get this error.

plot: [1,4] [=======>------------------------------------------] 16% est:28s Error in cor.test.default(x, y, method = method, use = use) : not enough finite observations In addition: There were 50 or more warnings (use warnings() to see the first 50)

I think this is in the ggplot pairs plots. Not sure what to do if there are no points in a panel.

For now it is a good choice to omit the ggpairs plot if there are all NAs present in one panel

markziemann commented 4 years ago

The data are too sparse. Currently the recommendation is mitch can only be used when >1000 genes are expressed in each contrast.