Producing slightly different results

[algebio]

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

[markrobinsonuzh]

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?

[algebio]

Hi

You were right. I missed that line... What a silly mistake! Thanks for your help.