plot.all.qc() - Error in unique.default(x, nmax = nmax)

[AnjaCaRa]

Hi Yoann,

after updating methview.qc() to version 0.027 and BiocompR to version 0.0.155 (Beta) I tried to run the plot.all.qc() function and the following error occured:

Describe the bug The plotting stopped at the log call of the fluorescence deviation heatmap and no fluorescence heatmap could be found wtihin the output directory. The following error was shown:

Plotting...
    Bisulfite Conversion I
    Bisulfite Conversion II
    Extension
    Hybridization
    Negative
    Non-polymorphic
    Norm A
    Norm C
    Norm G
    Norm T
    Specificity I
    Specificity II
    Staining
    Target Removal
    Genotyping probes heatmap
    Fluorescence deviation score heatmap
Error in unique.default(x, nmax = nmax) : 
  unique() applies only to vectors
In addition: There were 36 warnings (use warnings() to see them)

warnings() Warning messages: 1: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 2: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 3: Transformation introduced infinite values in continuous y-axis 4: Removed 2 rows containing non-finite values (stat_boxplot). 5: Transformation introduced infinite values in continuous y-axis 6: Removed 4 rows containing non-finite values (stat_boxplot). 7: In mclapply(X = DT.QC.meta[Target == target]$ID, mc.cores = ncores, ... : scheduled core 1 encountered error in user code, all values of the job will be affected 8: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 9: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 10: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 11: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 12: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 13: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 14: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 15: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 16: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 17: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 18: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 19: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 20: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 21: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 22: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 23: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 24: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 25: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 26: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 27: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 28: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 29: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 30: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 31: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 32: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 33: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 34: In FUN(X[[i]], ...) : Cy3 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 35: In FUN(X[[i]], ...) : Cy5 fluorescence intensity missing for probe IDs: 21630339, 24669308. Probes removed from final data.table. 36: In [.data.table(m, , :=(I, data.table::.I)) : Column 'I' does not exist to remove

To Reproduce

plot.all.qc(RnBSet = result, save.dir = "/////***/output/neuroblastoma/plots/methview.qc/Version0.0.27", ncores = 4, include.gp = TRUE, include.ds=TRUE)

You can find my script under the following DKFZ path: ////data//scripts/neuroblastoma/Methylation_Analysis/Quality_Control_Methview.qc_Package_1.R

Expected behavior The heatmap showing the fluorescence deviation for all QC probes should have been produced

Desktop (please complete the following information):

sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /usr/lib64/libblas.so.3.4.2 LAPACK: /usr/lib64/liblapack.so.3.4.2

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

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

other attached packages: [1] RnBeads.hg19_1.20.0 colorspace_2.0-2 ggsci_2.9
[4] methview.qc_0.0.27 BiocompR_0.0.155 RnBeads_2.6.0
[7] plyr_1.8.6 methylumi_2.34.0 minfi_1.34.0
[10] bumphunter_1.30.0 locfit_1.5-9.4 iterators_1.0.13
[13] foreach_1.5.1 Biostrings_2.56.0 XVector_0.28.0
[16] SummarizedExperiment_1.18.2 DelayedArray_0.14.1 FDb.InfiniumMethylation.hg19_2.2.0
[19] org.Hs.eg.db_3.11.4 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.40.1
[22] AnnotationDbi_1.50.3 reshape2_1.4.4 scales_1.1.1
[25] Biobase_2.48.0 illuminaio_0.30.0 matrixStats_0.60.0
[28] limma_3.44.3 gridExtra_2.3 gplots_3.1.1
[31] fields_12.5 viridis_0.6.1 viridisLite_0.4.0
[34] spam_2.7-0 dotCall64_1.0-1 ff_4.0.4
[37] bit_4.0.4 cluster_2.1.0 MASS_7.3-51.5
[40] GenomicRanges_1.40.0 GenomeInfoDb_1.24.2 IRanges_2.22.2
[43] S4Vectors_0.26.1 BiocGenerics_0.34.0 data.table_1.14.0
[46] ggplot2_3.3.5

loaded via a namespace (and not attached): [1] parallelDist_0.2.4 BiocFileCache_1.12.1 splines_4.0.0 BiocParallel_1.22.0 digest_0.6.27
[6] fansi_0.5.0 magrittr_2.0.1 memoise_2.0.0 tzdb_0.1.2 fastcluster_1.2.3
[11] readr_2.0.1 annotate_1.66.0 RcppParallel_5.1.4 askpass_1.1 siggenes_1.62.0
[16] prettyunits_1.1.1 blob_1.2.2 rappdirs_0.3.3 dplyr_1.0.7 crayon_1.4.1
[21] RCurl_1.98-1.3 genefilter_1.70.0 GEOquery_2.56.0 survival_3.1-12 glue_1.4.2
[26] gtable_0.3.0 zlibbioc_1.34.0 Rhdf5lib_1.10.1 maps_3.3.0 HDF5Array_1.16.1
[31] DBI_1.1.1 rngtools_1.5 Rcpp_1.0.7 xtable_1.8-4 progress_1.2.2
[36] mclust_5.4.7 preprocessCore_1.50.0 httr_1.4.2 RColorBrewer_1.1-2 ellipsis_0.3.2
[41] farver_2.1.0 pkgconfig_2.0.3 reshape_0.8.8 XML_3.99-0.6 dbplyr_2.1.1
[46] utf8_1.2.2 labeling_0.4.2 tidyselect_1.1.1 rlang_0.4.11 munsell_0.5.0
[51] tools_4.0.0 cachem_1.0.5 generics_0.1.0 RSQLite_2.2.7 ggdendro_0.1.22
[56] stringr_1.4.0 fastmap_1.1.0 bit64_4.0.5 beanplot_1.2 caTools_1.18.2
[61] scrime_1.3.5 purrr_0.3.4 nlme_3.1-147 doRNG_1.8.2 nor1mix_1.3-0
[66] xml2_1.3.2 biomaRt_2.44.4 compiler_4.0.0 rstudioapi_0.13 curl_4.3.2
[71] tibble_3.1.3 stringi_1.7.3 lattice_0.20-41 Matrix_1.2-18 multtest_2.44.0
[76] vctrs_0.3.8 pillar_1.6.2 lifecycle_1.0.0 bitops_1.0-7 rtracklayer_1.48.0
[81] R6_2.5.0 KernSmooth_2.23-16 codetools_0.2-16 gtools_3.9.2 assertthat_0.2.1
[86] rhdf5_2.32.4 openssl_1.4.4 withr_2.4.2 GenomicAlignments_1.24.0 Rsamtools_2.4.0
[91] GenomeInfoDbData_1.2.3 hms_1.1.0 quadprog_1.5-8 tidyr_1.1.3 base64_2.0
[96] DelayedMatrixStats_1.10.1

[YoannPa]

Alright, I will have a look at this. Btw there is no version 4.0.5 for BiocompR : latest version is still in beta 0.0.155

[AnjaCaRa]

Alright, I will have a look at this. Btw there is no version 4.0.5 for BiocompR : latest version is still in beta 0.0.155

True that, sorry accidently wrote down the R version instead of BiocompR version :D

[YoannPa]

Duplicate of #14

[YoannPa]

As you can see from the logs of plot.all.qc() the executing fails when generating Fluorescence deviation score heatmap. So it looks like the problem is coming from devscore.heatmap() and is actually the same issue as the one described in #14