I have experienced a strange error that I have not seen before in my years as an xcms user. The error comes from a C call in group.density so I have a hard time digging more into it my self.
When running a specific set of samples (38 LC-qTOF samples) I get the following error when i run group:
Error in rectUnique(groupmat[, c("mzmin", "mzmax", "rtmin", "rtmax"), :
NA/NaN/Inf in foreign function call (arg 1)
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
3: In min(x) : no non-missing arguments to min; returning Inf
4: In max(x) : no non-missing arguments to max; returning -Inf
> traceback()
9: .C("RectUnique", m, as.integer(order - 1), nr, nc, as.double(xdiff),
as.double(ydiff), logical(nrow(m)), DUP = FALSE, PACKAGE = "xcms")
8: rectUnique(groupmat[, c("mzmin", "mzmax", "rtmin", "rtmax"),
drop = FALSE], uorder)
7: .local(object, ...)
6: group.density(object, ...)
5: group.density(object, ...)
4: do.call(method, alist(object, ...))
3: .local(object, ...)
2: xcms::group(xset, mzwid = 0.1, bw = 10, minfrac = 0, minsamp = 0)
1: xcms::group(xset, mzwid = 0.1, bw = 10, minfrac = 0, minsamp = 0)
The parameters that provokes this is the combination of minsamp=0 and minfrac=0 - either alone works fine...
What happens is that a single row in the return from the C call contains inf and -inf instead of numbers.
Can anyone with insight into the C functions elaborate on what can cause a group to consist of inf?
best wishes
Thomas
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pepmaps_1.7-0 xlsx_0.5.0 xlsxjars_0.4.0 rJava_0.9-3 Rcpp_0.9.14
loaded via a namespace (and not attached):
[1] Biobase_2.18.0 BiocGenerics_0.4.0 Biostrings_2.26.0 caret_5.15-044 codetools_0.2-8 colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 ggdendro_0.1-07 ggplot2_0.9.2.1
[11] grid_2.15.1 gridExtra_0.9.1 gtable_0.1.1 IRanges_1.16.2 labeling_0.1 lattice_0.20-10 MASS_7.3-21 memoise_0.1 munsell_0.4 mzR_1.4.0
[21] OutlierD_1.22.0 parallel_2.15.1 pcaMethods_1.48.0 pcaPP_1.9-48 plyr_1.7.1 proto_0.3-9.2 RColorBrewer_1.0-5 reshape2_1.2.1 scales_0.2.2 stats4_2.15.1
[31] stringr_0.6.1 tools_2.15.1 xcms_1.34.0
Topic: Error with group.density