Error of xcmsSet with matchedfilter method

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Error of xcmsSet with matchedfilter method

November 15, 2016, 01:59:56 AM

Dear sir or madam,

when i use the xcmsSet with matchedfilter method, the problems were always existed. i am not sure what happened. Could anyone give help? Thanks! I used the window 7 systerm and 8 core CPU .

> traceback()
4: stop(.error_bplist(res))
3: bplapply(argList, findPeaksPar, BPPARAM = BPPARAM)
2: bplapply(argList, findPeaksPar, BPPARAM = BPPARAM)
1: xcmsSet(cdffiles, fwhm = 30, snthresh = 3, step = 0.1, steps = 1,
profmethod = "binlin")

> xset<-xcmsSet(cdffiles,fwhm = 30, snthresh = 3, step = 0.1, steps = 1,profmethod="binlin")
Loading required package: xcms
Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

IQR, mad, xtabs

The following objects are masked from 'package:base':

anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit, which, which.max, which.min

Loading required package: ProtGenerics
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

95:229 145:464 195:706 245:921 295:1116 345:1275 395:1391 445:1502 495:1606 545:1706 595:1806
95:226 145:461 195:698 245:910 295:1100 345:1253 395:1368 445:1475 495:1579 545:1679 595:1779
Error: BiocParallel errors
element index: 3, 4, 5, 6, 7, 8, ...
first error: 'from' cannot be NA, NaN or infinite
In addition: Warning message:
stop worker failed:
'clear_cluster' receive data failed:
reached elapsed time limit

Sincerely yours,
Hemi Luan
HKBU
Hong Kong

Re: Error of xcmsSet with matchedfilter method

Reply #1 – November 15, 2016, 02:17:31 AM

You'll probably need to supply a reproducible example (data) to get help for this.

Re: Error of xcmsSet with matchedfilter method

Reply #2 – November 15, 2016, 03:16:24 AM

Quote from: Jan Stanstrup – on November 15, 2016, 02:17:31 AM

You'll probably need to supply a reproducible example (data) to get help for this.

Thanks. Jan

Re: Error of xcmsSet with matchedfilter method

Reply #3 – November 15, 2016, 03:20:24 AM

Quote from: Jan Stanstrup – on November 15, 2016, 02:17:31 AM

You'll probably need to supply a reproducible example (data) to get help for this.

I have add a code
<< snowparam <- SnowParam(workers = 1, type = "SOCK")
<< set1a <- xcmsSet(cdffiles[1], method = "matchedFilter", fwhm = 3,snthresh = 3, BPPARAM = snowparam)

The BPPARAM problems seems to be disappeared. However, the other error was produced. I don't know how to fix it.

traceback()
13: stop(e)
12: value[[3L]](cond)
11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch({
   FUN(...)
   }, error = handle_error)
8: withCallingHandlers({
   tryCatch({
   FUN(...)
   }, error = handle_error)
   }, warning = handle_warning)
7: FUN(X[], ...)
6: lapply(X, FUN, ...)
5: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = param)
4: bplapply(X, FUN, ..., BPREDO = BPREDO, BPPARAM = param)
3: bplapply(argList, findPeaksPar, BPPARAM = BPPARAM)
2: bplapply(argList, findPeaksPar, BPPARAM = BPPARAM)
1: xcmsSet(cdffiles, method = "matchedFilter", fwhm = 3, snthresh = 3,
   BPPARAM = snowparam)

95:423 145:857 195:1267 245:1549 295:1737 345:1849 395:1867 445:1887 495:1905 545:1935 595:1951
95:453 145:909 195:1373 245:1755 295:2043 345:2231 395:2299 445:2339 495:2351 545:2357 595:2357
95:443 145:903 195:1365 245:1733 295:2003 345:2171 395:2233 445:2265 495:2277 545:2277 595:2277
Error in seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) * :
'from' cannot be NA, NaN or infinite
In addition: Warning messages:
1: In xcmsRaw(arg$file, profmethod = params$profmethod, profparam = params$profparam, :
There are identical scantimes.
2: In min(x) : no non-missing arguments to min; returning Inf
3: In max(x) : no non-missing arguments to max; returning -Inf

do you have any suggestion? Thanks

Sincerely yours,
Hemi

Re: Error of xcmsSet with matchedfilter method

Reply #4 – November 15, 2016, 03:26:03 AM

I am not sure this can be resolved without one of those files. Seems there is something strange about them.
"There are identical scantimes." seems to be the hint. That is quite strange how that is possible. Did you run several things at the same time (MS1, data-dependant scans etc)?

This seem similar: http://www.metabolomics-forum.com/index.php?topic=530.msg1675#msg1675
What XCMS version are you using?