I'm drawing a MCA plot using FactoMine R. I have data tables that look like this:
Met Aa Fn Pg Pi Tf Smut Ssob An Csput
C1 High N.S. N.S. N.S. High N.S. High High N.S.
C2 High N.S. Low High N.S. N.S. N.S. N.S. N.S.
C4 High High N.S. High N.S. N.S. High N.S. High
C6 N.S. N.S. High N.S. N.S. N.S. N.S. N.S. High
C9 Low Low Low Low Low High N.S. Low Low
C12 N.S. N.S. Low N.S. N.S. N.S. High N.S. High
###So I loaded my data
metabolites<-read.csv2('MCA24h_carbon.csv',dec='.')##all metabolites at 24h
###Named the column
metID<-metabolites$met
###Created a new matrix
newmet<-subset(metabolites,select=-c(Met))
### and the number of categories per variable
cats<- apply (newmet, 2, function(x) nlevels(as.factor(x)))
#and this is the output I get from the analysis:
structure(c(85L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L,
3L, 3L, 3L, 3L), .Names = c("Var", "Aa", "Fn", "Pg", "Pi", "Tf",
"Smut", "Ssob", "An", "Csput"))
This was my first red sign... Afterwards, I performed the MCA just to see what will I get and this was the code:
mca1=MCA(metabolites, graph=FALSE)
mca1$eig
mca1$var$coord
mca1$ind$coord
mca1_var_df=data.frame(mca1$var$coord, Variable=rep(names(cats), cats))
mca1_obs_df= data.frame(mca1$ind$coord)
Then I get the following in the console:
Error in data.frame(mca1$var$coord, Variable = rep(names(cats), cats)) :
arguments imply differing number of rows: 269, 254
I'm very new using R (as in 1 week) but I have experience using SAS... I have no idea what I am doing wrong and why R is fixing my data into the above structure (3L, 3L, 3L...) Does anyone have any idea on how to proceed?
