Error in chromPeaks(from)[, "is_filled"] : subscript out of bounds

[lecorguille]

Hello,

Error in chromPeaks(from)[, "is_filled"] : subscript out of bounds

We are getting this errors at different steps : xcms, CAMERA ...
An example : https://help.galaxyproject.org/t/error-occured-during-the-camera-step/3298/4

I don't know yet if it's an issue with Galaxy, ReadMSData, XCMS ...
Any idea?

Thanks by advance

[jorainer]

As always, that's a problem of xcms (my fault :)): I moved this column from chromPeaks to chromPeakData. Reason: the former is a numeric matrix, the latter a DataFrame. We need less memory if we encode the "is_filled" as a logical instead of a numeric. You can solve your problem in two ways:

Setting isFilledChrom = TRUE in the chromPeaks call will append this column to the returned matrix:

chromPeaks(from, isFilledChrom = TRUE)[, "is_filled"]

Alternatively, you could access chromPeakData(from)$is_filled.

[lecorguille]

Thanks for the quick answer.

But I don't use this function (or at least not directly)

The issue spot this function I wrote to chain XCMS3 and CAMERA

# This function retrieve a xset like object
#@author Gildas Le Corguille lecorguille@sb-roscoff.fr
getxcmsSetObject <- function(xobject) {
    # XCMS 1.x
    if (class(xobject) == "xcmsSet")
        return (xobject)
    # XCMS 3.x
    if (class(xobject) == "XCMSnExp") {
        # Get the legacy xcmsSet object
        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
        if (!is.null(xset@phenoData$sample_group))
            sampclass(xset) <- xset@phenoData$sample_group
        else
            sampclass(xset) <- "."
        return (xset)
    }
}

Do you know if it comes from this : xset <- as(xobject, 'xcmsSet') ?

[sneumann]

Any chance of getting an example data set and code snippet as minimal working example ?
Yours, Steffen

[lecorguille]

@yguitton, can we try to provide your dataset of 12 alg*.cdf

[jorainer]

Which version of xcms are you using? I don't see any call to chromPeaks(from)[, "is_filled"] in the current (dev) version.

[yguitton]

Hi all,
thanks for your help.

The files are available on zenodo.
I 've tried to create a R script, but it's not a working example...
#Issue 466
library(xcms)
TEMP<-tempdir()
download.file("https://zenodo.org/record/3631074/files/alg3.mzData", destfile=paste(TEMP,"alg3.mzData", sep="/"))
download.file("https://zenodo.org/record/3631074/files/alg7.mzData", destfile=paste(TEMP,"alg7.mzData", sep="/"))
download.file("https://zenodo.org/record/3631074/files/alg8.mzData", destfile=paste(TEMP,"alg8.mzData", sep="/"))
download.file("https://zenodo.org/record/3631074/files/alg9.mzData", destfile=paste(TEMP,"alg9.mzData", sep="/"))
download.file("https://zenodo.org/record/3631074/files/alg11.mzData", destfile=paste(TEMP,"alg11.mzData", sep="/"))

myfiles<-list.files(path=TEMP, pattern=".mzData")
raw_data <- readMSData(myfiles, mode = "onDisk")
mfp <- MatchedFilterParam(binSize = 0.5, fwhm = 15, max = 500, snthresh = 10, steps = 2)

##Check parameter
mfp

Perform the peak detection using matchecFilter on the files

res <- findChromPeaks(raw_data, param = mfp)
head(chromPeaks(res))

[jorainer]

Excellent! Thank you @yguitton !

Your code above works if you use myfiles <- list.files(path = TEMP, pattern = ".mzData", full.names = FALSE).

I did run the code above and got no error in xset <- as(res, "xcmsSet"). Might well be that the R/xcms version I am using has already a fix for this in it. My sessionInfo:

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] xcms_3.8.2          MSnbase_2.12.0      ProtGenerics_1.18.0
 [4] S4Vectors_0.24.4    mzR_2.20.0          Rcpp_1.0.4.6       
 [7] BiocParallel_1.20.1 Biobase_2.46.0      BiocGenerics_0.32.0
[10] BiocManager_1.30.10

loaded via a namespace (and not attached):
 [1] RColorBrewer_1.1-2     DEoptimR_1.0-8         compiler_3.6.3        
 [4] pillar_1.4.3           plyr_1.8.6             iterators_1.0.12      
 [7] zlibbioc_1.32.0        digest_0.6.25          ncdf4_1.17            
[10] MALDIquant_1.19.3      lifecycle_0.2.0        tibble_3.0.1          
[13] preprocessCore_1.48.0  gtable_0.3.0           lattice_0.20-41       
[16] pkgconfig_2.0.3        rlang_0.4.5            Matrix_1.2-18         
[19] foreach_1.5.0          dplyr_0.8.5            IRanges_2.20.2        
[22] vctrs_0.2.4            multtest_2.42.0        grid_3.6.3            
[25] tidyselect_1.0.0       robustbase_0.93-6      glue_1.4.0            
[28] impute_1.60.0          R6_2.4.1               survival_3.1-12       
[31] XML_3.99-0.3           RANN_2.6.1             limma_3.42.2          
[34] ggplot2_3.3.0          purrr_0.3.3            magrittr_1.5          
[37] splines_3.6.3          scales_1.1.0           pcaMethods_1.78.0     
[40] codetools_0.2-16       ellipsis_0.3.0         MASS_7.3-51.5         
[43] MassSpecWavelet_1.52.0 mzID_1.24.0            assertthat_0.2.1      
[46] colorspace_1.4-1       affy_1.64.0            doParallel_1.0.15     
[49] munsell_0.5.0          vsn_3.54.0             crayon_1.3.4          
[52] affyio_1.56.0         

So, with xcms version >= 3.8.2 you should be OK - which version of xcms do you have?

[jsaintvanne]

Hi @jorainer ,

We are using xcms 3.4.4 and I tried with xcms 3.8.1 and it looks that works ! So we probably have to update the xcms version of Galaxy

[jorainer]

If possible I suggest to update the R to the most recent one (4.0.0) - with this one you will also have the most recent version of Bioconductor (3.11).

[yguitton]

Ok for me with xcms 3.8.2 and R 4.0.0

`>sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C LC_TIME=French_France.1252

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] metaMS_1.22.0 CAMERA_1.43.2 xcms_3.8.2 MSnbase_2.13.4 ProtGenerics_1.19.3 S4Vectors_0.25.15
[7] mzR_2.21.1 Rcpp_1.0.4.6 BiocParallel_1.21.3 Biobase_2.47.3 BiocGenerics_0.33.3

loaded via a namespace (and not attached):
[1] bitops_1.0-6 matrixStats_0.56.0 doParallel_1.0.15 RColorBrewer_1.1-2
[5] GenomeInfoDb_1.23.17 tools_4.0.0 backports_1.1.6 R6_2.4.1
[9] affyio_1.57.0 rpart_4.1-15 Hmisc_4.4-0 colorspace_1.4-1
[13] nnet_7.3-13 gridExtra_2.3 compiler_4.0.0 MassSpecWavelet_1.53.0
[17] preprocessCore_1.49.2 graph_1.65.3 cli_2.0.2 htmlTable_1.13.3
[21] DelayedArray_0.13.12 scales_1.1.0 checkmate_2.0.0 DEoptimR_1.0-8
[25] robustbase_0.93-6 affy_1.65.1 RBGL_1.63.1 stringr_1.4.0
[29] digest_0.6.25 foreign_0.8-76 XVector_0.27.2 base64enc_0.1-3
[33] jpeg_0.1-8.1 pkgconfig_2.0.3 htmltools_0.4.0 limma_3.43.8
[37] htmlwidgets_1.5.1 rlang_0.4.5 rstudioapi_0.11 impute_1.61.0
[41] mzID_1.25.0 acepack_1.4.1 RCurl_1.98-1.2 magrittr_1.5
[45] GenomeInfoDbData_1.2.3 Formula_1.2-3 MALDIquant_1.19.3 Matrix_1.2-18
[49] munsell_0.5.0 fansi_0.4.1 lifecycle_0.2.0 vsn_3.55.0
[53] stringi_1.4.6 yaml_2.2.1 SummarizedExperiment_1.17.5 MASS_7.3-51.5
[57] zlibbioc_1.33.1 plyr_1.8.6 grid_4.0.0 crayon_1.3.4
[61] lattice_0.20-41 splines_4.0.0 multtest_2.43.1 knitr_1.28
[65] pillar_1.4.3 igraph_1.2.5 GenomicRanges_1.39.3 codetools_0.2-16
[69] XML_3.99-0.3 glue_1.4.0 latticeExtra_0.6-29 pcaMethods_1.79.1
[73] data.table_1.12.8 BiocManager_1.30.10 png_0.1-7 vctrs_0.2.4
[77] foreach_1.5.0 gtable_0.3.0 RANN_2.6.1 assertthat_0.2.1
[81] ggplot2_3.3.0 xfun_0.13 ncdf4_1.17 survival_3.1-12
[85] tibble_3.0.0 snow_0.4-3 iterators_1.0.12 IRanges_2.21.8
[89] cluster_2.1.0 ellipsis_0.3.0 `

[yguitton]

@jorainer it's working for xcms 3.8.2 BUT isn't with xcms 3.9.1

I get that

'> myfiles<-list.files(path=TEMP, pattern=".mzData", full.names=FALSE)
> setwd(TEMP)
> raw_data <- readMSData(myfiles, mode = "onDisk")
> mfp <- MatchedFilterParam(binSize = 0.5, fwhm = 15, max = 500, snthresh = 10, steps = 2)
> ##Check parameter
> mfp
Object of class:  MatchedFilterParam 
Parameters:
 binSize: 0.5 
Error in (function (classes, fdef, mtable)  : 
   unable to find an inherited method for function ‘impute’ for signature ‘"MatchedFilterParam"’'

any Idea ?
Yann

[jorainer]

I guess the generic definition of the impute method was moved from one to another package. I suggest that you bring all your packages up-to-date by calling BiocManager::install(), then it should work again. Also, this should install a more recent version of xcms (currently we have 3.9.5).

[yguitton]

@jorainer my problem is solved, Many Thanks.
Now we have to see how to deal with our initial issue under Galaxy. I'm pretty sure @lecorguille will find some magic.

[jorainer]

Just let me know if you need help

[jorainer]

Closing the issue now. Feel free to re-open if needed.