Producing slightly different results
Closed this issue · 2 comments
Hi Mark
I have just installed and run the pipeline with the default dataset on a different computer. I have compared the figures with those from the F1000 and I'm getting slightly different results from figure 5 included onward including tables from the differential analysis.
I have checked possible errors during installation but everything seems to be fine.
What could be the reason?
Regards
Juan
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices
[6] utils datasets methods base
other attached packages:
[1] scater_1.14.6
[2] SingleCellExperiment_1.8.0
[3] diffcyt_1.6.1
[4] ggplot2_3.2.1
[5] cowplot_1.0.0
[6] CATALYST_1.10.1
[7] readxl_1.3.1
[8] HDCytoData_1.6.6
[9] flowCore_1.52.1
[10] SummarizedExperiment_1.16.1
[11] DelayedArray_0.12.2
[12] BiocParallel_1.20.1
[13] matrixStats_0.55.0
[14] Biobase_2.46.0
[15] GenomicRanges_1.38.0
[16] GenomeInfoDb_1.22.0
[17] IRanges_2.20.2
[18] S4Vectors_0.24.3
[19] ExperimentHub_1.12.0
[20] AnnotationHub_2.18.0
[21] BiocFileCache_1.10.2
[22] dbplyr_1.4.2
[23] BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] utf8_1.1.4
[2] shinydashboard_0.7.1
[3] R.utils_2.9.2
[4] ks_1.11.7
[5] lme4_1.1-21
[6] tidyselect_1.0.0
[7] RSQLite_2.2.0
[8] AnnotationDbi_1.48.0
[9] htmlwidgets_1.5.1
[10] grid_3.6.2
[11] Rtsne_0.15
[12] munsell_0.5.0
[13] codetools_0.2-16
[14] DT_0.12
[15] withr_2.1.2
[16] colorspace_1.4-1
[17] flowViz_1.50.0
[18] knitr_1.28
[19] rstudioapi_0.11
[20] flowClust_3.24.0
[21] robustbase_0.93-6
[22] openCyto_1.24.0
[23] labeling_0.3
[24] GenomeInfoDbData_1.2.2
[25] mnormt_1.5-6
[26] farver_2.0.3
[27] bit64_0.9-7
[28] flowWorkspace_3.34.1
[29] vctrs_0.2.2
[30] TH.data_1.0-10
[31] xfun_0.12
[32] R6_2.4.1
[33] ggbeeswarm_0.6.0
[34] clue_0.3-57
[35] rsvd_1.0.3
[36] locfit_1.5-9.1
[37] bitops_1.0-6
[38] assertthat_0.2.1
[39] promises_1.1.0
[40] scales_1.1.0
[41] multcomp_1.4-12
[42] beeswarm_0.2.3
[43] gtable_0.3.0
[44] sandwich_2.5-2
[45] rlang_0.4.4
[46] GlobalOptions_0.1.1
[47] splines_3.6.2
[48] lazyeval_0.2.2
[49] hexbin_1.28.1
[50] shinyBS_0.61
[51] BiocManager_1.30.10
[52] yaml_2.2.1
[53] reshape2_1.4.3
[54] abind_1.4-7
[55] httpuv_1.5.2
[56] IDPmisc_1.1.20
[57] RBGL_1.62.1
[58] tools_3.6.2
[59] ellipsis_0.3.0
[60] RColorBrewer_1.1-2
[61] ggridges_0.5.2
[62] Rcpp_1.0.3
[63] plyr_1.8.5
[64] base64enc_0.1-3
[65] zlibbioc_1.32.0
[66] purrr_0.3.3
[67] RCurl_1.98-1.1
[68] FlowSOM_1.18.0
[69] viridis_0.5.1
[70] GetoptLong_0.1.8
[71] zoo_1.8-8
[72] haven_2.2.0
[73] ggrepel_0.8.1
[74] cluster_2.1.0
[75] fda_2.4.8
[76] magrittr_1.5
[77] RSpectra_0.16-0
[78] ncdfFlow_2.32.0
[79] data.table_1.12.8
[80] openxlsx_4.1.4
[81] circlize_0.4.8
[82] mvtnorm_1.1-0
[83] shinyjs_1.1
[84] hms_0.5.3
[85] mime_0.9
[86] xtable_1.8-4
[87] XML_3.99-0.3
[88] rio_0.5.16
[89] jpeg_0.1-8.1
[90] mclust_5.4.5
[91] gridExtra_2.3
[92] shape_1.4.4
[93] ggcyto_1.14.0
[94] compiler_3.6.2
[95] ellipse_0.4.1
[96] tibble_2.1.3
[97] flowStats_3.44.0
[98] KernSmooth_2.23-16
[99] crayon_1.3.4
[100] minqa_1.2.4
[101] R.oo_1.23.0
[102] htmltools_0.4.0
[103] corpcor_1.6.9
[104] pcaPP_1.9-73
[105] later_1.0.0
[106] tidyr_1.0.2
[107] rrcov_1.5-2
[108] RcppParallel_4.4.4
[109] DBI_1.1.0
[110] ComplexHeatmap_2.2.0
[111] MASS_7.3-51.5
[112] rappdirs_0.3.1
[113] boot_1.3-24
[114] Matrix_1.2-18
[115] car_3.0-6
[116] cli_2.0.1
[117] R.methodsS3_1.8.0
[118] igraph_1.2.4.2
[119] forcats_0.4.0
[120] pkgconfig_2.0.3
[121] foreign_0.8-75
[122] plotly_4.9.2
[123] vipor_0.4.5
[124] XVector_0.26.0
[125] drc_3.0-1
[126] stringr_1.4.0
[127] digest_0.6.24
[128] RcppAnnoy_0.0.14
[129] tsne_0.1-3
[130] ConsensusClusterPlus_1.50.0
[131] graph_1.64.0
[132] cellranger_1.1.0
[133] uwot_0.1.5
[134] edgeR_3.28.0
[135] DelayedMatrixStats_1.8.0
[136] curl_4.3
[137] shiny_1.4.0
[138] gtools_3.8.1
[139] nloptr_1.2.1
[140] rjson_0.2.20
[141] nlme_3.1-144
[142] lifecycle_0.1.0
[143] jsonlite_1.6.1
[144] carData_3.0-4
[145] BiocNeighbors_1.4.1
[146] fansi_0.4.1
[147] viridisLite_0.3.0
[148] limma_3.42.2
[149] pillar_1.4.3
[150] lattice_0.20-38
[151] fastmap_1.0.1
[152] httr_1.4.1
[153] plotrix_3.7-7
[154] DEoptimR_1.0-8
[155] survival_3.1-8
[156] interactiveDisplayBase_1.24.0
[157] glue_1.3.1
[158] zip_2.0.4
[159] png_0.1-8
[160] BiocVersion_3.10.1
[161] bit_1.1-15.2
[162] Rgraphviz_2.30.0
[163] stringi_1.4.6
[164] nnls_1.4
[165] blob_1.2.1
[166] BiocSingular_1.2.2
[167] CytoML_1.12.0
[168] latticeExtra_0.6-29
[169] memoise_1.1.0
[170] dplyr_0.8.4
[171] irlba_2.3.3
One quick check: do you run RNGversion("3.5.3") at the start of your script?
If yes, can you expand on what "slightly different" means?
Hi
You were right. I missed that line... What a silly mistake! Thanks for your help.