Hello everybody,
I’m trying to use MicrobiomeAnalystR to print a PCA.
This errors allways show up, and I can’t find where those NA are. Theys are not in my data sets.
Thank you.
library (“MicrobiomeAnalystR”)
mbSet<-Init.mbSetObj()
[1] “Init MicrobiomeAnalyst!”
Warning message:
In Cairo::CairoFonts(“Arial:style=Regular”, “Arial:style=Bold”, :
CairoFonts() has no effect on Windows. Please use par(family=“…”) to specify the desired font - see ?par.
mbSet<-SetModuleType(mbSet, “mdp”)
mbSet<-ReadSampleTable(mbSet, “Tabla_PCA_CONTROL_MET.csv”);
Warning message:
In FUN(newX[, i], …) : NAs introduced by coercion
mbSet<-Read16SAbundData(mbSet, “Tabla_PCA_CONTROL_OTU.csv”,“text”,“SILVA”,“T”,“false”);
mbSet<-SanityCheckData(mbSet, “text”);
[1] “Sanity check passed!”
mbSet<-SanityCheckSampleData(mbSet);
mbSet<-SetMetaAttributes(mbSet, “1”)
Warning message:
In FUN(if (length(d.call) < 2L) newX[, 1] else array(newX[, 1L], :
** NAs introduced by coercion**
mbSet<-PlotLibSizeView(mbSet, “norm_libsizes_0”,“png”);
mbSet<-CreatePhyloseqObj(mbSet, “text”,“SILVA”,“T” , “false”)
Warning messages:
1: In type.convert.default(X[[i]], …) :
‘as.is’ should be specified by the caller; using TRUE
2: In type.convert.default(X[[i]], …) :
‘as.is’ should be specified by the caller; using TRUE
3: In type.convert.default(X[[i]], …) :
‘as.is’ should be specified by the caller; using TRUE
4: In type.convert.default(X[[i]], …) :
‘as.is’ should be specified by the caller; using TRUE
5: In type.convert.default(X[[i]], …) :
‘as.is’ should be specified by the caller; using TRUE
6: In type.convert.default(X[[i]], …) :
‘as.is’ should be specified by the caller; using TRUE
mbSet<-ApplyAbundanceFilter(mbSet, “prevalence”, 4, 0.2);
mbSet<-ApplyVarianceFilter(mbSet, “iqr”, 0.1);
mbSet<-PerformNormalization(mbSet, “none”, “colsum”, “none”, “true”);
mbSet<-PerformBetaDiversity(mbSet, “beta_diver_2”,“PCoA”,“bray”,“expfac”,“BodySite”,“none”,“OTU”,“Not_Assigned_1”,“Chao1”, “yes”, “adonis”, “png”, 72, “default”, “false”);
Error in vegdist(c(11253.3954210322, 5363.65586783952, 0, 3746.16018580955, : **
** missing values are not allowed with argument ‘na.rm = FALSE’