Hello everyone,
I hope you are having a great day.
So I am using MetaboAnalystR to process some of the data.
I have a problem with plotting the PCA graph.
So basically upon doing the “SanityCheck” I got the info that:
mSet<-SanityCheckData(tmp)
[1] “Successfully passed sanity check!”
[2] “Samples are not paired.”
[3] “2 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.”
[6] “All data values are numeric.”
[7] “<font color="red"> 23 features with a constant or single value across samples were found and deleted.”
[8] “A total of 214 (4.6%) missing values were detected.”
[9] “By default, missing values will be replaced by 1/5 of min positive values of their corresponding variables”
[10] “Click the Proceed button if you accept the default practice;”
[11] “Or click the Missing Values button to use other methods.”
However when I want to plot the PCA graph I get:
tmp ← PlotPCAPairSummary(tmp, imgName = “1”, pc.num = 10)
Error in legend(“bottom”, legend = legend.nm, pch = pchs.def, col = col.def, :
‘legend’ is of length 0
Could you please help,
Thank you
PS
I am begginer/intermediate when it comes to coding so I would really really appreciate in details explenation
Thanks!!!