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
I found a possible bug and implement a workaround and some checking routines. I deployed v1.9.7 to BioC.
Perhaps you could give me an update if this fix the problem.
Carsten
It can take up to 24 hours until the bioconductor page shows the updated version, since it only builds the package once a day.
Ahh...got it. I will keep my eyes out.
Krista
The changes to CAMERA version 1.9.7 now allow me to process my data without any errors.
Thanks for the help & new program version,
Krista