Errors with multiple MicrobiomeAnalystR functions

[ScottWrigley]

Hi Dr. Xia and team - I hope your projects are going well.

I am using MicrobiomeAnalystR (package version 2.0); R version 4.4.0 (2024-04-24); Rstudio version 2024.9.0.375.

First, let me point out that I have been able to successfully run numerous functions in MicrobiomeAnalystR, including:

• creating the mbSet PhyloseqObj and running the sanity check
• filtering (ApplyAbundanceFilter)
• normalizing (PerformNormalization)
• visualize taxa bar plot (PlotTaxaAundanceBar)
• run alpha diversity (PlotAlphaData, etc.)
• run beta diversity (PerformBetaDiversity, etc.)
• run differential abundance using LEfSe (PerformLefseAnal)

However, in attempting to run single-factor comparisons using Mann-Whitney/Kruskal-Wallis and EdgeR, and run multifactor comparisons using MaAsLin, the MicrobiomeAnalystR functions produce errors.

- Function: PerformUnivarTest

Code: mbSet<-PerformUnivarTest(mbSet, "ldl_cat",0.05,"NA","Phylum","nonpar", "Above_Optimal", "Normal");

Error: Error in if (!is.null(mbSetObj$analSet$rnaseq$resTable.edger.all) & mbSetObj[["analSet"]][["var.type"]] == : argument is of length zero

- Function: PerformRNAseqDE

Code: mbSet<-PerformRNAseqDE(mbSet, "EdgeR",0.05,"ldl_cat","NA","Phylum",0.0, "Above_Optimal", "Normal");

Error: Error in .perform_edger(variable, data, p.lvl, fc.thresh, comp1, comp2) :
object 'mbSetObj' not found

- Function: ProcessMaaslin

Code: mbSet<-ProcessMaaslin(mbSet, "ldl_cat", "false", "Normal", "Above_Optimal", "NA", "Genus" , "ZINB" ,"covariate_plot_0.png" , 0.05)

Error: Error in ProcessMaaslin(mbSet, "ldl_cat", "false", "Normal", "Above_Optimal", :
could not find function "ProcessMaaslin"

I appreciate any guidance you can provide.

-Scott

[ScottWrigley]

Issue never addressed.