__STDOUT LOG__ Job runs on fgcz-h-166 at /scratch/PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41_temp2134592 Starting EzAppPostSamsa2Analysis PostSamsa2Analysis PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41_temp2134592 2024-12-13 10:46:48 mkdir orgresults mkdir funcresults cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/08_003_a.RefSeq.annotated_org.txt orgresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/08_003_b.RefSeq.annotated_org.txt orgresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/08_006_a.RefSeq.annotated_org.txt orgresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/08_006_b.RefSeq.annotated_org.txt orgresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/13_019_a.RefSeq.annotated_org.txt orgresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/13_019_b.RefSeq.annotated_org.txt orgresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/13_022_a.RefSeq.annotated_org.txt orgresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/13_022_b.RefSeq.annotated_org.txt orgresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/08_003_a.RefSeq.annotated_func.txt funcresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/08_003_b.RefSeq.annotated_func.txt funcresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/08_006_a.RefSeq.annotated_func.txt funcresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/08_006_b.RefSeq.annotated_func.txt funcresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/13_019_a.RefSeq.annotated_func.txt funcresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/13_019_b.RefSeq.annotated_func.txt funcresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/13_022_a.RefSeq.annotated_func.txt funcresults/ cp /srv/GT/analysis/course_sushi/public/gstore/projects/p8002/Samsa2_2023-12-12--09-57-04/13_022_b.RefSeq.annotated_func.txt funcresults/ [1] "08_003_a.RefSeq.annotated_org.txt" "08_003_b.RefSeq.annotated_org.txt" [3] "08_006_a.RefSeq.annotated_org.txt" "08_006_b.RefSeq.annotated_org.txt" [5] "13_019_a.RefSeq.annotated_org.txt" "13_019_b.RefSeq.annotated_org.txt" [7] "13_022_a.RefSeq.annotated_org.txt" "13_022_b.RefSeq.annotated_org.txt" [[1]] [1] "p8002/Samsa2_2023-12-12--09-57-04/08_003_a.RefSeq.annotated.txt" [[2]] [1] "p8002/Samsa2_2023-12-12--09-57-04/08_006_a.RefSeq.annotated.txt" [[3]] [1] "p8002/Samsa2_2023-12-12--09-57-04/13_019_a.RefSeq.annotated.txt" [[4]] [1] "p8002/Samsa2_2023-12-12--09-57-04/13_022_a.RefSeq.annotated.txt" [1] "08_003_a.RefSeq.annotated.txt" "08_006_a.RefSeq.annotated.txt" [3] "13_019_a.RefSeq.annotated.txt" "13_022_a.RefSeq.annotated.txt" [1] "before" [1] "Medication" [1] "08_003_a" "08_006_a" "13_019_a" "13_022_a" [1] "08_003_a.RefSeq.annotated_org.txt" "08_006_a.RefSeq.annotated_org.txt" [3] "13_019_a.RefSeq.annotated_org.txt" "13_022_a.RefSeq.annotated_org.txt" [1] "08_003_a.RefSeq.annotated_func.txt" "08_003_b.RefSeq.annotated_func.txt" [3] "08_006_a.RefSeq.annotated_func.txt" "08_006_b.RefSeq.annotated_func.txt" [5] "13_019_a.RefSeq.annotated_func.txt" "13_019_b.RefSeq.annotated_func.txt" [7] "13_022_a.RefSeq.annotated_func.txt" "13_022_b.RefSeq.annotated_func.txt" [[1]] [1] "p8002/Samsa2_2023-12-12--09-57-04/08_003_a.RefSeq.annotated.txt" [[2]] [1] "p8002/Samsa2_2023-12-12--09-57-04/08_006_a.RefSeq.annotated.txt" [[3]] [1] "p8002/Samsa2_2023-12-12--09-57-04/13_019_a.RefSeq.annotated.txt" [[4]] [1] "p8002/Samsa2_2023-12-12--09-57-04/13_022_a.RefSeq.annotated.txt" [1] "08_003_a.RefSeq.annotated.txt" "08_006_a.RefSeq.annotated.txt" [3] "13_019_a.RefSeq.annotated.txt" "13_022_a.RefSeq.annotated.txt" [1] "before" [1] "Medication" [1] "08_003_a" "08_006_a" "13_019_a" "13_022_a" [1] "08_003_a.RefSeq.annotated_func.txt" "08_006_a.RefSeq.annotated_func.txt" [3] "13_019_a.RefSeq.annotated_func.txt" "13_022_a.RefSeq.annotated_func.txt" rename s/_/-/g */*.txt rename s/control-/control_/g */*.txt rename s/experimental-/experimental_/g */*.txt bash /usr/local/ngseq/src/samsa2/R_scripts/run_all_Rscripts.sh orgresults/ [1] "USAGE: $ diversity_stats.R -I working_directory/ " Working directory is orgresults/ [1] "USAGE: $ diversity_graphs.R -I working_directory/ -O save.filename" Working directory is orgresults/ Saving diversity graphs as diversity_graph.rds Success! Saving diversity graphs as diversity_graph.rds now. [1] "USAGE: $ get_raw_counts_table.R -I working_directory/ -O save.filename" Working directory is orgresults/ [1] "WARNING: no raw counts file specified, skipping this info for DESeq analysis." Now saving raw counts table as raw_counts_table.tab [1] "USAGE: $ get_normalized_counts_table.R -I working_directory/ -O save.filename" Working directory is orgresults/ [1] "WARNING: no raw counts file specified, skipping this info for DESeq analysis." Success! Saving normalized counts table as normalized_counts_table.tab [1] "USAGE: $ run_DESeq_stats.R -I working_directory/ -O save.filename" Working directory is orgresults/ [1] "WARNING: no raw counts file specified, skipping this info for DESeq analysis." Success! Saving results file as DESeq_results.tab [1] "USAGE: $ run_DESeq_stats.R -I working_directory/ -O save.filename -L level (1,2,3,4)" Working directory is orgresults/ Saving results as PCA_plot.tab.rds Calculating DESeq results for hierarchy level Saving PCA plot as PCA_plot.tab.rds now. [1] "USAGE: $ make_DESeq_heatmap -I working_directory/ -O save.filename -N number of row entries (50)" Working directory is orgresults/ Saving results as DESeq_heatmap.rds Loading packages, may take a second... [1] "./control_08-006-a.RefSeq.annotated-org.txt" [1] "./control_13-019-a.RefSeq.annotated-org.txt" [1] "./control_13-022-a.RefSeq.annotated-org.txt" [1] "./experimental_08-006-b.RefSeq.annotated-org.txt" [1] "./experimental_13-019-b.RefSeq.annotated-org.txt" [1] "./experimental_13-022-b.RefSeq.annotated-org.txt" Calculating DESeq results, may take a second... Saving heatmap matrix as DESeq_heatmap.rds now. [1] "USAGE: $ make_volcano_plot.R -D working_directory/ -O save.filename -G title -F fc_cutoff -P p_cutoff -C TRUE" Working directory is orgresults/ Saving results as volcano_plot.rds Organism.Name baseMean controlMean experimentalMean log2FoldChange 1 Gardnerella_vaginalis 110795.95 221429.4446 162.45997 -10.411879 2 Atopobium_vaginae 39036.60 78030.6405 42.56275 -10.838573 3 Lactobacillus_iners 27905.58 38004.9791 17806.18294 -1.093779 4 Lactobacillus_crispatus 27350.63 167.0251 54534.23224 8.350538 5 Prevotella_timonensis 27171.72 54338.6582 4.78552 -13.491174 6 Sneathia_sanguinegens 22050.82 44091.3249 10.31104 -12.062553 lfcSE stat pvalue padj 1 1.482041 -7.0253661 2.135058e-12 3.335617e-10 2 1.532069 -7.0744689 1.500222e-12 3.046952e-10 3 1.816425 -0.6021601 5.470676e-01 5.885033e-01 4 1.897534 4.4007315 1.078866e-05 1.565126e-04 5 1.562553 -8.6340575 5.921322e-18 1.202620e-14 6 1.621621 -7.4385783 1.017746e-13 3.445071e-11 'data.frame': 6214 obs. of 3 variables: $ Organism.Name : chr "Gardnerella_vaginalis" "Atopobium_vaginae" "Lactobacillus_iners" "Lactobacillus_crispatus" ... $ log2FoldChange: num -10.41 -10.84 -1.09 8.35 -13.49 ... $ padj : num 3.34e-10 3.05e-10 5.89e-01 1.57e-04 1.20e-14 ... Organism.Name log2FoldChange padj Length:6214 Min. :-28.414 Min. :0.000 Class :character 1st Qu.: -5.309 1st Qu.:0.015 Mode :character Median : -2.215 Median :0.069 Mean : -3.384 Mean :0.151 3rd Qu.: -0.746 3rd Qu.:0.164 Max. : 8.351 Max. :0.998 NA's :4183 Saving volcano plot as volcano_plot.rds now. [1] "USAGE: $ make_combined_graphs.R -D working_directory/ -O save.filename -N org_number -G title" Working directory is orgresults/ Saving results as combined_graphs_ctrl_vs_exp.rds Saving PCA plot as combined_graphs_ctrl_vs_exp.rds now. [1] "USAGE: $ make_combined_graphs.R -D working_directory/ -O save.filename -N org_number -G title" Working directory is orgresults/ Saving results as combined_graph.rds Saving PCA plot as combined_graph.rds now. bash /usr/local/ngseq/src/samsa2/R_scripts/run_all_Rscripts.sh funcresults/ [1] "USAGE: $ diversity_stats.R -I working_directory/ " Working directory is funcresults/ [1] "USAGE: $ diversity_graphs.R -I working_directory/ -O save.filename" Working directory is funcresults/ Saving diversity graphs as diversity_graph.rds Success! Saving diversity graphs as diversity_graph.rds now. [1] "USAGE: $ get_raw_counts_table.R -I working_directory/ -O save.filename" Working directory is funcresults/ [1] "WARNING: no raw counts file specified, skipping this info for DESeq analysis." Now saving raw counts table as raw_counts_table.tab [1] "USAGE: $ get_normalized_counts_table.R -I working_directory/ -O save.filename" Working directory is funcresults/ [1] "WARNING: no raw counts file specified, skipping this info for DESeq analysis." Success! Saving normalized counts table as normalized_counts_table.tab [1] "USAGE: $ run_DESeq_stats.R -I working_directory/ -O save.filename" Working directory is funcresults/ [1] "WARNING: no raw counts file specified, skipping this info for DESeq analysis." Success! Saving results file as DESeq_results.tab [1] "USAGE: $ run_DESeq_stats.R -I working_directory/ -O save.filename -L level (1,2,3,4)" Working directory is funcresults/ Saving results as PCA_plot.tab.rds Calculating DESeq results for hierarchy level Saving PCA plot as PCA_plot.tab.rds now. [1] "USAGE: $ make_DESeq_heatmap -I working_directory/ -O save.filename -N number of row entries (50)" Working directory is funcresults/ Saving results as DESeq_heatmap.rds Loading packages, may take a second... [1] "./control_08-006-a.RefSeq.annotated-func.txt" [1] "./control_13-019-a.RefSeq.annotated-func.txt" [1] "./control_13-022-a.RefSeq.annotated-func.txt" [1] "./experimental_08-006-b.RefSeq.annotated-func.txt" [1] "./experimental_13-019-b.RefSeq.annotated-func.txt" [1] "./experimental_13-022-b.RefSeq.annotated-func.txt" Calculating DESeq results, may take a second... Saving heatmap matrix as DESeq_heatmap.rds now. [1] "USAGE: $ make_volcano_plot.R -D working_directory/ -O save.filename -G title -F fc_cutoff -P p_cutoff -C TRUE" Working directory is funcresults/ Saving results as volcano_plot.rds Organism.Name baseMean controlMean experimentalMean 1 hypothetical_protein 80774.331 46101.7831 115446.879 2 endonuclease 14121.237 989.7758 27252.698 3 hypothetical_protein,_partial 13926.065 3844.9564 24007.173 4 endonuclease,_partial 6183.703 426.2335 11941.172 5 DUF1725_domain-containing_protein 3808.706 220.3964 7397.015 6 MULTISPECIES:_hypothetical_protein 3043.785 1520.1283 4567.442 log2FoldChange lfcSE stat pvalue padj 1 1.324326 0.8107434 1.633471 1.023699e-01 0.1653467831 2 4.783128 1.1689789 4.091714 4.281961e-05 0.0004512678 3 2.642386 0.9413343 2.807065 4.999522e-03 0.0169829290 4 4.808114 1.2127208 3.964733 7.347827e-05 0.0006798575 5 5.068714 1.2028384 4.213961 2.509308e-05 0.0003022730 6 1.587031 0.6973693 2.275740 2.286160e-02 0.0540078726 'data.frame': 4783 obs. of 3 variables: $ Organism.Name : chr "hypothetical_protein" "endonuclease" "hypothetical_protein,_partial" "endonuclease,_partial" ... $ log2FoldChange: num 1.32 4.78 2.64 4.81 5.07 ... $ padj : num 0.165347 0.000451 0.016983 0.00068 0.000302 ... Organism.Name log2FoldChange padj Length:4783 Min. :-23.0541 Min. :0.0000 Class :character 1st Qu.: -3.2391 1st Qu.:0.0110 Mode :character Median : -0.8009 Median :0.0803 Mean : -0.9680 Mean :0.2014 3rd Qu.: 0.8944 3rd Qu.:0.2884 Max. : 22.9867 Max. :0.9993 NA's :2558 Saving volcano plot as volcano_plot.rds now. [1] "USAGE: $ make_combined_graphs.R -D working_directory/ -O save.filename -N org_number -G title" Working directory is funcresults/ Saving results as combined_graphs_ctrl_vs_exp.rds Saving PCA plot as combined_graphs_ctrl_vs_exp.rds now. [1] "USAGE: $ make_combined_graphs.R -D working_directory/ -O save.filename -N org_number -G title" Working directory is funcresults/ Saving results as combined_graph.rds Saving PCA plot as combined_graph.rds now. ezRun tag: 81a203b2a83152a315eaa7463292c4b4d9afaa20 ezRun github link: https://github.com/uzh/ezRun/tree/81a203b2a83152a315eaa7463292c4b4d9afaa20 R version 4.4.0 (2024-04-24) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] 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 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: Europe/Zurich tzcode source: system (glibc) attached base packages: [1] stats4 stats graphics grDevices utils datasets methods [8] base other attached packages: [1] htmltools_0.5.8.1 DT_0.33 [3] pheatmap_1.0.12 rmarkdown_2.27 [5] vegan_2.6-6.1 lattice_0.22-6 [7] permute_0.9-7 scales_1.3.0 [9] reshape2_1.4.4 plyr_1.8.9 [11] optparse_1.7.5 knitr_1.47 [13] gridExtra_2.3 genefilter_1.86.0 [15] RColorBrewer_1.1-3 EnhancedVolcano_1.22.0 [17] ggrepel_0.9.5 DESeq2_1.44.0 [19] SummarizedExperiment_1.34.0 Biobase_2.64.0 [21] MatrixGenerics_1.16.0 matrixStats_1.3.0 [23] ezRun_3.19.1 lubridate_1.9.3 [25] forcats_1.0.0 stringr_1.5.1 [27] dplyr_1.1.4 purrr_1.0.2 [29] readr_2.1.5 tidyr_1.3.1 [31] tibble_3.2.1 ggplot2_3.5.1 [33] tidyverse_2.0.0 GenomicRanges_1.56.1 [35] Biostrings_2.72.1 GenomeInfoDb_1.40.1 [37] XVector_0.44.0 IRanges_2.38.0 [39] S4Vectors_0.42.0 BiocGenerics_0.50.0 [41] data.table_1.15.4 loaded via a namespace (and not attached): [1] DBI_1.2.3 rlang_1.1.4 magrittr_2.0.3 [4] compiler_4.4.0 RSQLite_2.3.7 mgcv_1.9-1 [7] png_0.1-8 vctrs_0.6.5 pkgconfig_2.0.3 [10] crayon_1.5.2 fastmap_1.2.0 labeling_0.4.3 [13] utf8_1.2.4 tzdb_0.4.0 UCSC.utils_1.0.0 [16] bit_4.0.5 xfun_0.45 zlibbioc_1.50.0 [19] cachem_1.1.0 jsonlite_1.8.8 blob_1.2.4 [22] highr_0.11 DelayedArray_0.30.1 BiocParallel_1.38.0 [25] parallel_4.4.0 cluster_2.1.6 R6_2.5.1 [28] bslib_0.7.0 stringi_1.8.4 jquerylib_0.1.4 [31] Rcpp_1.0.12 Matrix_1.7-0 splines_4.4.0 [34] timechange_0.3.0 tidyselect_1.2.1 yaml_2.3.8 [37] abind_1.4-5 codetools_0.2-20 withr_3.0.0 [40] KEGGREST_1.44.0 evaluate_0.24.0 survival_3.7-0 [43] getopt_1.20.4 pillar_1.9.0 plotly_4.10.4 [46] generics_0.1.3 hms_1.1.3 munsell_0.5.1 [49] xtable_1.8-4 glue_1.7.0 lazyeval_0.2.2 [52] tools_4.4.0 annotate_1.82.0 locfit_1.5-9.9 [55] XML_3.99-0.16.1 grid_4.4.0 crosstalk_1.2.1 [58] AnnotationDbi_1.66.0 colorspace_2.1-1 nlme_3.1-165 [61] GenomeInfoDbData_1.2.12 cli_3.6.2 fansi_1.0.6 [64] viridisLite_0.4.2 S4Arrays_1.4.1 gtable_0.3.5 [67] sass_0.4.9 digest_0.6.35 SparseArray_1.4.8 [70] farver_2.1.2 htmlwidgets_1.6.4 memoise_2.0.1 [73] lifecycle_1.0.4 httr_1.4.7 bit64_4.0.5 [76] MASS_7.3-61 Finished EzAppPostSamsa2Analysis PostSamsa2Analysis PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41_temp2134592 2024-12-13 10:50:19 [1] "/scratch/PostSamsa2Analysis_after--over--before_2024-12-13--10-46-41_temp2134592/PostSamsa2Analysis/00index.html" __SCRIPT END__ __STDERR LOG__ Loading required package: data.table Loading required package: Biostrings Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:data.table’: first, second The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: expand.grid, I, unname Loading required package: IRanges Attaching package: ‘IRanges’ The following object is masked from ‘package:data.table’: shift Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: ‘Biostrings’ The following object is masked from ‘package:base’: strsplit Loading required package: GenomicRanges Loading required package: tidyverse ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ── ✔ dplyr 1.1.4 ✔ readr 2.1.5 ✔ forcats 1.0.0 ✔ stringr 1.5.1 ✔ ggplot2 3.5.1 ✔ tibble 3.2.1 ✔ lubridate 1.9.3 ✔ tidyr 1.3.1 ✔ purrr 1.0.2 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ lubridate::%within%() masks IRanges::%within%() ✖ dplyr::between() masks data.table::between() ✖ dplyr::collapse() masks Biostrings::collapse(), IRanges::collapse() ✖ dplyr::combine() masks BiocGenerics::combine() ✖ purrr::compact() masks XVector::compact() ✖ dplyr::desc() masks IRanges::desc() ✖ tidyr::expand() masks S4Vectors::expand() ✖ dplyr::filter() masks stats::filter() ✖ dplyr::first() masks S4Vectors::first(), data.table::first() ✖ lubridate::hour() masks data.table::hour() ✖ lubridate::isoweek() masks data.table::isoweek() ✖ dplyr::lag() masks stats::lag() ✖ dplyr::last() masks data.table::last() ✖ lubridate::mday() masks data.table::mday() ✖ lubridate::minute() masks data.table::minute() ✖ lubridate::month() masks data.table::month() ✖ ggplot2::Position() masks BiocGenerics::Position(), base::Position() ✖ lubridate::quarter() masks data.table::quarter() ✖ purrr::reduce() masks GenomicRanges::reduce(), IRanges::reduce() ✖ dplyr::rename() masks S4Vectors::rename() ✖ lubridate::second() masks S4Vectors::second(), data.table::second() ✖ lubridate::second<-() masks S4Vectors::second<-() ✖ dplyr::slice() masks XVector::slice(), IRanges::slice() ✖ purrr::transpose() masks data.table::transpose() ✖ lubridate::wday() masks data.table::wday() ✖ lubridate::week() masks data.table::week() ✖ lubridate::yday() masks data.table::yday() ✖ lubridate::year() masks data.table::year() ℹ Use the conflicted package () to force all conflicts to become errors unknown param: partition unknown param: sushi_app unknown param: isLastJob Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: ‘matrixStats’ The following object is masked from ‘package:dplyr’: count Attaching package: ‘MatrixGenerics’ The following objects are masked from ‘package:matrixStats’: colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: ‘Biobase’ The following object is masked from ‘package:MatrixGenerics’: rowMedians The following objects are masked from ‘package:matrixStats’: anyMissing, rowMedians Loading required package: ggrepel Attaching package: ‘genefilter’ The following objects are masked from ‘package:MatrixGenerics’: rowSds, rowVars The following objects are masked from ‘package:matrixStats’: rowSds, rowVars The following object is masked from ‘package:readr’: spec Attaching package: ‘gridExtra’ The following object is masked from ‘package:Biobase’: combine The following object is masked from ‘package:dplyr’: combine The following object is masked from ‘package:BiocGenerics’: combine ------------------------------------------------------------------------------ You have loaded plyr after dplyr - this is likely to cause problems. If you need functions from both plyr and dplyr, please load plyr first, then dplyr: library(plyr); library(dplyr) ------------------------------------------------------------------------------ Attaching package: ‘plyr’ The following object is masked from ‘package:matrixStats’: count The following objects are masked from ‘package:dplyr’: arrange, count, desc, failwith, id, mutate, rename, summarise, summarize The following object is masked from ‘package:purrr’: compact The following object is masked from ‘package:XVector’: compact The following object is masked from ‘package:IRanges’: desc The following object is masked from ‘package:S4Vectors’: rename Attaching package: ‘reshape2’ The following object is masked from ‘package:tidyr’: smiths The following objects are masked from ‘package:data.table’: dcast, melt Attaching package: ‘scales’ The following object is masked from ‘package:purrr’: discard The following object is masked from ‘package:readr’: col_factor Loading required package: permute Loading required package: lattice This is vegan 2.6-6.1 Loading required package: rmarkdown converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Warning message: In sparseTest(counts(object, normalized = TRUE), 0.9, 100, 0.1) : the rlog assumes that data is close to a negative binomial distribution, an assumption which is sometimes not compatible with datasets where many genes have many zero counts despite a few very large counts. In this data, for 10.2% of genes with a sum of normalized counts above 100, it was the case that a single sample's normalized count made up more than 90% of the sum over all samples. the threshold for this warning is 10% of genes. See plotSparsity(dds) for a visualization of this. We recommend instead using the varianceStabilizingTransformation or shifted log (see vignette). using ntop=500 top features by variance converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship -- note: fitType='parametric', but the dispersion trend was not well captured by the function: y = a/x + b, and a local regression fit was automatically substituted. specify fitType='local' or 'mean' to avoid this message next time. final dispersion estimates fitting model and testing Warning message: Removed 1 row containing missing values or values outside the scale range (`geom_bar()`). converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing using ntop=500 top features by variance converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing Warning message: Removed 1 row containing missing values or values outside the scale range (`geom_bar()`). Warning messages: 1: ggrepel: 855 unlabeled data points (too many overlaps). Consider increasing max.overlaps 2: ggrepel: 940 unlabeled data points (too many overlaps). Consider increasing max.overlaps