Hello.
I am continuously receiving the following error message when running the RemoveMissingByPercent function: “Error in colMeans(is.na(int.mat)) : ‘x’ must be an array of at least two dimensions”. It appears that for some reason my data is not being added into the mSet matrix properly and I am not sure how to fix this. This was previously working fine but last week began throwing this error. The full code to this point is below:
> mSet<-InitDataObjects("conc", "stat", FALSE, 150)
Starting Rserve...
"C:\Users\path..."
[1] "MetaboAnalyst R objects initialized ..."
Warning message:
In Cairo::CairoFonts(regular = "Arial:style=Regular", bold = "Arial:style=Bold", :
CairoFonts() has no effect on Windows. Please use par(family="...") to specify the desired font - see ?par.
> mSet<-Read.TextData(mSet, "C:/Users/path.../metabolites.csv",
+ "rowu", "disc")
> mSet$msgSet$read.msg
[1] "Samples are in rows and features in columns"
[2] "The uploaded file is in comma separated values (.csv) format."
[3] "The uploaded data file contains 116 (samples) by 965 (compounds) data matrix."
> mSet <- SanityCheckData(mSet)
[1] "Successfully passed sanity check!"
[2] "Samples are not paired."
[3] "4 groups were detected in samples."
[4] "Only English letters, numbers, underscore, hyphen and forward slash (/) are allowed."
[5] "<font color=\"orange\">Other special characters or punctuations (if any) will be stripped off.</font>"
[6] "<font color=\"red\">Non-numeric values were found and replaced by NA.</font>"
[7] "<font color=\"red\"> 25 features with a constant or single value across samples were found and deleted.</font>"
[8] ""
[9] "A total of 30721 (28.2%) missing values were detected."
There were 26 warnings (use warnings() to see them)
> mSet <- RemoveMissingByPercent(mSet, percent=0.2)
Error in colMeans(is.na(int.mat)) :
'x' must be an array of at least two dimensions
Any help is appreciated!
