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I have a phyloseq object with 4000+ taxa and 300+ samples.

What methods/packages can I use to perform feature selection to reduce the number of taxa/OTUs prior to performing random forest? I was hoping to check correlations between different taxa.

I'm planning to use the taxa as predictors of disease (i.e., disease~.).

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    $\begingroup$ Welcome to Cross Validated! What do you hope to accomplish with variable selection? $\endgroup$
    – Dave
    May 12 at 12:51
  • $\begingroup$ Questions solely about how software works are off-topic here, but you may have a real statistical question buried here. You may want to edit your question to clarify the underlying statistical issue. You may find that when you understand the statistical concepts involved, the software-specific elements are self-evident or at least easy to get from the documentation. $\endgroup$
    – kjetil b halvorsen ♦
    May 12 at 23:45

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