Error on zero treatment

[chiehchangchen]

Hello Stefanie, Thanks for your cool package. I am quite new in network analysis and R. I was trying using netconstruct on my own dataset. However, error developed when I used zeroMethod="multRepl", but not zeroMethod="pseudo" . Would you help me to work out the problem?

The codes ad error messages are the following: "> net <- netConstruct(physeq,

• measure = "pearson",
• normMethod = "clr",
• zeroMethod = "multRepl",
• sparsMethod = "threshold",
• thresh = 0.3,
• verbose = 3) 8799 taxa and 84 samples remaining.

Zero treatment: Execute multRepl() ... Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': Column(s) containing all zeros/unobserved values were found (check it out using zPatterns).

[stefpeschel]

Hey,

Apparently, this error occurs if there are samples whose sum of counts is zero, which can't be handled by the multRepl() function of zCompositions package. You can solve this issue by setting NetCoMi's filters appropriately, e.g.:

netConstruct(physeq, 
   filtSamp = "totalReads",
   filtSampPar = list(totalReads = 500),
   measure = "pearson",
   normMethod = "clr", 
   zeroMethod = "multRepl",
   sparsMethod = "threshold", 
   thresh = 0.3,
   verbose = 3)

Please see the help page of netConstruct for possible values.

The next update will include a bug fix to catch samples with an overall sum of zero. But for now, setting filters should solve this issue.

Please reopen this issue, if the error still occurs.

Best, Stefanie