Hello,
I am trying to use CAMERA with LC-MS (FT-ICR) data, and have an interesting problem. Oddly, this problem is only appearing in one ionization mode, so it is apparently a data dependent problem. However, I can't figure out where the problem begins. The actual problem comes while I am at the groupCorr step.
By this point, I have done:
xgN<-group.nearest(xs)
xgF <-fillPeaks(xgN,method = "chrom")
xsa <-xsAnnotate(xgF)
xsaF <-groupFWHM(xsa)
xsaFI <-findIsotopes(xsaF)
xsaC <-groupCorr(xsaFI,cor_eic_th=0.75,pval=0.05, graphMethod="hcs",
calcIso = TRUE, calcCiS = TRUE, calcCaS = FALSE)
I then get an error after 'calculating isotope assignments in 290 groups'. The error is:
% finished: Error in rbind(resMat, cbind(x = tmp2[, 1], y = tmp2[, 2], cor = 1, ps = i)) :
number of columns of matrices must match (see arg 2)
traceback() says:
rbind(resMat, cbind(x = tmp2[, 1], y = tmp2[, 2], cor = 1, ps = i))
8: calcIsotopes(object)
7: calcIsotopes(object)
6: .local(object, cor_eic_th, pval, graphMethod, calcIso, calcCiS,
calcCaS, psg_list, ...)
5: groupCorr(xsaFI, cor_eic_th = 0.75, pval = 0.05, graphMethod = "hcs",
calcIso = TRUE, calcCiS = TRUE, calcCaS = FALSE)
4: groupCorr(xsaFI, cor_eic_th = 0.75, pval = 0.05, graphMethod = "hcs",
calcIso = TRUE, calcCiS = TRUE, calcCaS = FALSE)
3: eval.with.vis(expr, envir, enclos)
2: eval.with.vis(ei, envir)
1: source("Tps4c_pos.r")
If I set calcIso=FALSE, then the analysis proceeds without error.
I have also tried going back a step and running groupCorr on the data without the isotope information, and then it notes there is not isotope/isotope annotation (which makes sense), but the analysis goes to completion:
xsaF <-groupFWHM(xsa)
xsaC <-groupCorr(xsaF,cor_eic_th=0.75,pval=0.05, graphMethod="hcs", calcIso = TRUE, calcCiS = TRUE, calcCaS = FALSE)
There is apparently something happening at the findIsotope step, but I have been trying different parameters with no luck. I suppose I could just use the calcIso=FALSE results, but since I was able to get this to work in negative ion mode, I am perplexed.
I am running:
CAMERA 1.8.2
xcms 1.26.1
R 2.13.1
Any thoughts and/or places where I should be looking?
Thanks in advance,
Krista