CAMERA Peaklist table is empty

ZandkarimiF commented 4 years ago

Hi,

I am trying to use CAMERA (version 1.45.1) to annotate peacklists generated by XCMS (3.11.3) in R (version 4.0.0). But, the generated peaklist is empty. Please see below for more details. I am not sure which parts I am doing wrong. Thanks for your help. Fereshteh ######## xset <- as(xdata5, "xcmsSet") xset <- group(xset) xset<-fillPeaks(xset) library(CAMERA)

an <- xsAnnotate(xset, sample=seq(1,length(sampnames(xset))), nSlaves=4) Attaching package: ‘snow’ The following objects are masked from ‘package:BiocGenerics’:clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, parApply, parCapply, parLapply, parRapply, parSapply The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, clusterSplit, makeCluster, parApply, parCapply, parLapply, parRapply, parSapply, splitIndices, stopCluster Starting snow cluster with 4 local sockets. Run clean parallel after processing to remove the spawned slave processes!

an <- groupFWHM(an) Start grouping after retention time. Created 453 pseudospectra.

an <- findIsotopes(an) Generating peak matrix! Run isotope peak annotation % finished: 10 20 30 40 50 60 70 80 90 100
Found isotopes: 2845

an <- groupCorr(an, graphMethod="lpc", calcIso = TRUE, calcCiS = TRUE, calcCaS = TRUE, cor_eic_th=0.5) _ Calculating peak correlations in 453 Groups... % finished: 10 20 30 40 50 60 70 80 90 100
Generating EIC's ..

Calculating peak correlations in 453 Groups... % finished: 10 20 30 40 50 60 70 80 90 100
Generating EIC's ..

Calculating peak correlations in 453 Groups... % finished: 10 20 30 40 50 60 70 80 90 100

Calculating peak correlations across samples. % finished: 10 20 30 40 50 60 70 80 90 100

Calculating isotope assignments in 453 Groups... % finished: 10 20 30 40 50 60 70 80 90 100
Calculating graph cross linking in 453 Groups... % finished: 10 20 30 40 50 60 70 80 90 100
New number of ps-groups: 667 xsAnnotate has now 667 groups, instead of 453 _

ann.add<-findAdducts(an, ppm = 5,mzabs = 0.015, multiplier = 2,polarity = "negative") _Generating peak matrix for peak annotation!

Calculating possible adducts in 667 Groups... Parallel mode: There are 77 tasks. Calculating possible adducts in 667 Groups... Parallel mode: There are 77 tasks. Sending task # 1 Sending task # 2 Sending task # 3 Sending task # 4 Sending task # 5 Sending task # 6 Sending task # 7 Sending task # 8 Sending task # 9 Sending task # 10 Sending task # 11 Sending task # 12 Sending task # 13 Sending task # 14 Sending task # 15 Sending task # 16 Sending task # 17 Sending task # 18 Sending task # 19 Sending task # 20 Sending task # 21 Sending task # 22 Sending task # 23 Sending task # 24 Sending task # 25 Sending task # 26 Sending task # 27 Sending task # 28 Sending task # 29 Sending task # 30 Sending task # 31 Sending task # 32 Sending task # 33 Sending task # 34 Sending task # 35 Sending task # 36 Sending task # 37 Sending task # 38 Sending task # 39 Sending task # 40 Sending task # 41 Sending task # 42 Sending task # 43 Sending task # 44 Sending task # 45 Sending task # 46 Sending task # 47 Sending task # 48 Sending task # 49 Sending task # 50 Sending task # 51 Sending task # 52 Sending task # 53 Sending task # 54 Sending task # 55 Sending task # 56 Sending task # 57 Sending task # 58 Sending task # 59 Sending task # 60 Sending task # 61 Sending task # 62 Sending task # 63 Sending task # 64 Sending task # 65 Sending task # 66 Sending task # 67 Sending task # 68 Sending task # 69 Sending task # 70 Sending task # 71 Sending task # 72 Sending task # 73 Sending task # 74 Sending task # 75 Sending task # 76 Sending task # 77

Warning message: Use of 'xcmsClusterApply' is deprecated! Use 'BPPARAM' arguments instead. _ peaklist<-getPeaklist(ann.add) write.csv(sample,file="Neg-annotations_CAMERA.csv") ##########

korseby commented 4 years ago

Can you post your SessionInfo()? On which operating system are you? Using snow for parallel processing is outdated with R 4 I think. You should use one of the options to BPPARAM instead. Can you test without parallelization?

ZandkarimiF commented 4 years ago

My operating system is Windows 10. Yes, I have tried without parallelization, and it didn't work again. The generated peaklist is empty. Here is my SessionInfo:

sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] CAMERA_1.45.1 dplyr_1.0.0 SummarizedExperiment_1.19.5 DelayedArray_0.15.4 matrixStats_0.56.0 Matrix_1.2-18
[7] GenomicRanges_1.41.5 GenomeInfoDb_1.25.2 IRanges_2.23.10 xcms_3.11.3 MSnbase_2.15.2 ProtGenerics_1.21.0
[13] S4Vectors_0.27.12 Biobase_2.49.0 BiocParallel_1.23.0 pheatmap_1.0.12 magrittr_1.5 RColorBrewer_1.1-2
[19] pander_0.6.3 mzR_2.23.0 Rcpp_1.0.4.6 BiocGenerics_0.35.4

loaded via a namespace (and not attached): [1] bitops_1.0-6 doParallel_1.0.15 backports_1.1.8 tools_4.0.0 R6_2.4.1 affyio_1.59.0 rpart_4.1-15
[8] Hmisc_4.4-0 colorspace_1.4-1 nnet_7.3-14 tidyselect_1.1.0 gridExtra_2.3 compiler_4.0.0 MassSpecWavelet_1.55.0 [15] preprocessCore_1.51.0 graph_1.67.1 htmlTable_1.13.3 checkmate_2.0.0 scales_1.1.1 DEoptimR_1.0-8 robustbase_0.93-6
[22] affy_1.67.0 RBGL_1.65.0 stringr_1.4.0 digest_0.6.25 foreign_0.8-80 XVector_0.29.2 htmltools_0.5.0
[29] base64enc_0.1-3 jpeg_0.1-8.1 pkgconfig_2.0.3 limma_3.45.7 htmlwidgets_1.5.1 rlang_0.4.6 rstudioapi_0.11
[36] impute_1.63.0 generics_0.0.2 mzID_1.27.0 acepack_1.4.1 RCurl_1.98-1.2 GenomeInfoDbData_1.2.3 Formula_1.2-3
[43] MALDIquant_1.19.3 munsell_0.5.0 lifecycle_0.2.0 vsn_3.57.0 stringi_1.4.6 MASS_7.3-51.6 zlibbioc_1.35.0
[50] plyr_1.8.6 grid_4.0.0 crayon_1.3.4 lattice_0.20-41 splines_4.0.0 knitr_1.28 pillar_1.4.4
[57] igraph_1.2.5 codetools_0.2-16 XML_3.99-0.3 glue_1.4.1 latticeExtra_0.6-29 data.table_1.12.8 pcaMethods_1.81.0
[64] BiocManager_1.30.10 vctrs_0.3.1 png_0.1-7 foreach_1.5.0 gtable_0.3.0 RANN_2.6.1 purrr_0.3.4
[71] ggplot2_3.3.2 xfun_0.14 ncdf4_1.17 survival_3.2-3 tibble_3.0.1 snow_0.4-3 iterators_1.0.12
[78] cluster_2.1.0 ellipsis_0.3.1

ZandkarimiF commented 4 years ago

I also tried it on a UINIX server (Platform: x86_64-pc-linux-gnu (64-bit). I am using one of the cluster's high memory nodes (512 GB) with 24 processors and R version 4.0.1. But can't get any results for CAMERA! Could you tell me what I am doing wrong in the following codes?

register(SerialParam()) xset <- as(xdata5, "xcmsSet") xset <- group(xset) xset<-fillPeaks(xset) library(CAMERA) an <- xsAnnotate(xset, sample=seq(1,length(sampnames(xset))))

an <- groupFWHM(an) an <- findIsotopes(an) an <- groupCorr(an, graphMethod="lpc", calcIso = TRUE, calcCiS = TRUE, calcCaS = TRUE, cor_eic_th=0.5)

This step took more than 10 hrs!!!

ann.add<-findAdducts(an, ppm = 5,mzabs = 0.015, multiplier = 2,polarity = "negative") peaklist<-getPeaklist(ann.add) write.csv(peaklist,file="Neg-annotations_CAMERA.csv")

Thanks for your suggestions and help --Fereshteh

sneumann commented 4 years ago

Hi, is that an issue with CAMERA, or specific to your data set ? Can you run the examples provided with CAMERA ? Could you post information about your show(xdata5) and about show(ann.add) ? Yours, Steffen

sneumann / CAMERA

CAMERA Peaklist table is empty #58