groupCorr, calcIso = TRUE

September 20, 2011, 01:02:18 PM

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:

Code: [Select]

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:

Code: [Select]

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

Re: groupCorr, calcIso = TRUE

Reply #1 – September 23, 2011, 04:59:56 AM

Hi Krista,

the calcIso parameter triggers if recognized isotopes should get a higher score in the graph separation.
I take a look into it, but it could be, that I need one example file to reproduce the failure.

I'll come back to you in case.

Carsten

Re: groupCorr, calcIso = TRUE

Reply #2 – September 23, 2011, 06:36:07 AM

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

Re: groupCorr, calcIso = TRUE

Reply #3 – September 23, 2011, 08:35:27 AM

Hi Carsten,

Thanks for looking into this.

I could easily be missing something here, but when I look through BioConductor, I only find CAMERA version 1.9.6 - and I did check that, the error still appears with that version.

Krista

Re: groupCorr, calcIso = TRUE

Reply #4 – September 23, 2011, 09:32:06 AM

It can take up to 24 hours until the bioconductor page shows the updated version, since it only builds the package once a day.

Re: groupCorr, calcIso = TRUE

Reply #5 – September 23, 2011, 09:44:53 AM

Ahh...got it. I will keep my eyes out.

Krista

Re: groupCorr, calcIso = TRUE

Reply #6 – September 26, 2011, 08:50:54 AM

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