sampleQC.biplot() - Error in [.data.table(loadings.data, , :=(2:3, lapply(X = data.table::.SD, :

[AnjaCaRa]

Hi Yoann, after updating methview.qc() to version 0.027 and BiocompR to version 0.0.155 (Beta) I tried to run the sampleQC.biplot() function and the following error occured:

Describe the bug I don't receive a PCA plot anymore

To Reproduce plot3<-sampleQC.biplot(RnBSet = result, PCx = 1, PCy = 2, loadings = TRUE, loadings.col = "blue", point.size = 2.5, color.data ='TMM', shape.data = NULL)

Error in [.data.table(loadings.data, , :=(2:3, lapply(X = data.table::.SD, : Supplied 2 columns to be assigned an empty list (which may be an empty data.table or data.frame since they are lists too). To delete multiple columns use NULL instead. To add multiple empty list columns, use list(list()). In addition: 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.

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

Expected behavior A PCA plot should be generated

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
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C 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
[3] ggsci_2.9 methview.qc_0.0.27
[5] BiocompR_0.0.155 RnBeads_2.6.0
[7] plyr_1.8.6 methylumi_2.34.0
[9] minfi_1.34.0 bumphunter_1.30.0
[11] locfit_1.5-9.4 iterators_1.0.13
[13] foreach_1.5.1 Biostrings_2.56.0
[15] XVector_0.28.0 SummarizedExperiment_1.18.2
[17] 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 [21] GenomicFeatures_1.40.1 AnnotationDbi_1.50.3
[23] reshape2_1.4.4 scales_1.1.1
[25] Biobase_2.48.0 illuminaio_0.30.0
[27] matrixStats_0.60.0 limma_3.44.3
[29] gridExtra_2.3 gplots_3.1.1
[31] fields_12.5 viridis_0.6.1
[33] viridisLite_0.4.0 spam_2.7-0
[35] dotCall64_1.0-1 ff_4.0.4
[37] bit_4.0.4 cluster_2.1.0
[39] MASS_7.3-51.5 GenomicRanges_1.40.0
[41] GenomeInfoDb_1.24.2 IRanges_2.22.2
[43] S4Vectors_0.26.1 BiocGenerics_0.34.0
[45] data.table_1.14.0 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
[5] digest_0.6.27 fansi_0.5.0 magrittr_2.0.1 memoise_2.0.0
[9] tzdb_0.1.2 fastcluster_1.2.3 readr_2.0.1 annotate_1.66.0
[13] RcppParallel_5.1.4 askpass_1.1 siggenes_1.62.0 prettyunits_1.1.1
[17] 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
[25] glue_1.4.2 gtable_0.3.0 zlibbioc_1.34.0 Rhdf5lib_1.10.1
[29] maps_3.3.0 HDF5Array_1.16.1 DBI_1.1.1 rngtools_1.5
[33] Rcpp_1.0.7 xtable_1.8-4 progress_1.2.2 mclust_5.4.7
[37] 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
[45] dbplyr_2.1.1 utf8_1.2.2 labeling_0.4.2 tidyselect_1.1.1
[49] rlang_0.4.11 munsell_0.5.0 tools_4.0.0 cachem_1.0.5
[53] generics_0.1.0 RSQLite_2.2.7 ggdendro_0.1.22 stringr_1.4.0
[57] 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
[65] nor1mix_1.3-0 xml2_1.3.2 biomaRt_2.44.4 compiler_4.0.0
[69] rstudioapi_0.13 curl_4.3.2 tibble_3.1.3 stringi_1.7.3
[73] lattice_0.20-41 Matrix_1.2-18 multtest_2.44.0 vctrs_0.3.8
[77] 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
[85] assertthat_0.2.1 rhdf5_2.32.4 openssl_1.4.4 withr_2.4.2
[89] GenomicAlignments_1.24.0 Rsamtools_2.4.0 GenomeInfoDbData_1.2.3 hms_1.1.0
[93] quadprog_1.5-8 tidyr_1.1.3 base64_2.0 DelayedMatrixStats_1.10.1

Additional context Add any other context about the problem here.

[YoannPa]

The issue was coming from data.table synthax issues in BiocompR. Please install the latest version of BiocompR (0.0.156). If that doesn't solve your issue, feel free to reopen the issue.