Error message "error in resMat"

August 27, 2013, 07:55:43 AM

Hi,

We encountered an error message when using our 'routine' CAMERA script, at the peak correlations step. Please see below:

> library(CAMERA)
> diffreport <- annotateDiffreport(xset3)
Start grouping after retention time.
Created 292 pseudospectra.
Generating peak matrix!
Run isotope peak annotation
% finished: 10 40 50 60 70 80 90 100
Found isotopes: 894
Start grouping after correlation.
Generating EIC's ..

Calculating peak correlations in 292 Groups...
% finished: 10 40 Erreur dans resMat[cnt, ] <- c(xi, yi, res$r[row, col], i) :
indice hors limites
De plus : Messages d'avis :
1: sd(<matrix>) is deprecated.
Use apply(*, 2, sd) instead.
2: sd(<matrix>) is deprecated.
Use apply(*, 2, sd) instead.
3: In data.row.names(row.names, rowsi, i) :
some row.names duplicated: 29,2546,2606,2674,2679,2725,2769,2778,2823,2826,2837,2857,2920,2966 --> row.names NOT used
> write.csv(diffreport, file="diffreport.csv")
Erreur dans as.data.frame.default(x[], optional = TRUE) :
cannot coerce class 'structure("standardGeneric", package = "methods")' into a data.frame

It's in French, but easy to translate: "error in resMat ... index above limits".
Would someone have any idea about where we went wrong ? We used this script for months with no problem so far. Our .cdf files are much heavier than before (40 000 Ko vs. 4 000Ko before), but I can see any link. And moreover, the XCMS script is working perfectly fine on the very same dataset...

Thanks a lot,
Gaelle.