Skip to main content
Topic: xcms - error in row.names (Read 2055 times) previous topic - next topic

xcms - error in row.names

I saw numerous post about errors in row.names with xcms but I didn't find a solution.
This is my script with my problem :

#Packages
library(Biobase)
library(xcms)
library(multtest)
library(ade4)
library(RVAideMemoire)

#Peakpicking (I have low res data so I use matchedFilter)
xset<-xcmsSet(method="matchedFilter",step=0.2,steps=2,mzdiff=0.4,
              fwhm=30,snthresh=10)
#alignement
xset<-group(xset,bw=30,minfrac=0.5, mzwid=0.25,max=50,sleep=0)
#time correction
xset2<-retcor(xset,method="obiwarp",plottype=c("deviation"),profStep=1)
#alignement
> xset3<-group(xset2,bw=10,minfrac=0.5,mzwid=0.25,max=50,sleep=0)
#fillpeaks
xset4<-fillPeaks(xset3)
#report table
reporttab <- diffreport(xset4, "QC", "blanc", "MatriceBC",
                        1000,metlin = 0, h=480, w=640)
In data.row.names(row.names, rowsi, i) :
  some row.names duplicated: 651,746,866,2311,2609,3828,6151,6579,6632,7542,7874,8143,8597,er --> row.names NOT used

The row.names correspond to the first column of my matrice (number). I think that the duplicated row.names are removed of my matrice. Indeed, I don't see duplicate row.names in my matrice and it's write "NOT used" in the warning message.
I have multiples files (160) in different folders but all the filename are different. I think that there is a problem with the alignment.

Do you know how to solve this error and why row.names duplicated appears?

Thank you so much,
HAPPY NEW YEAR :)

Isis.

 

Re: xcms - error in row.names

Reply #1
Can you make a minimum reproducible example?
Is the warning from diffreport?
I don't know what it tries to put in the row names. Searching the forum it seems this is an old problem. Best way to get it resolved is to make an example (+ the data) that can be reproduced and post on the xcms github issues page.

The warning however should not be a big deal as it is only about assigning row names. The warning says it simply gives up assigning row names.
Blog: stanstrup.github.io