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"source": "proBatch.Rmd", "filename": "proBatch.html", "title": "proBatch", "author": "| Jelena Čuklina, Chloe H. Lee, Patrick Pedrioli and Ruedi Aebersold | Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Switzerland", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Batch effects analysis in large-scale data", "Analysis of large-scale data: steps before and after batch correction", "Preparation for the analysis", "IInstallation", "Preparing the data for analysis", "Loading the libraries", "Input data formats", "Example dataset", "Preparing sample and peptide annotations", "Defining the order of samples from running date and time", "Generating peptide annotation from OpenSWATH data", "Other utility functions", "Transforming the data to long or wide format", "Transforming the data to log scale", "Defining the color scheme", "Step-by-step workflow", "Initial assessment of the raw data matrix", "Plotting the sample mean", "Plotting boxplots", "Normalization", "Median normalization", "Quantile normalization", "Diagnostics of batch effects in normalized data", "Hierarchical clustering", "Principal component analysis (PCA)", "Principal variance component analysis (PVCA)", "Peptide-level diagnostics and spike-ins", "Correction of batch effects", "Continuous drift correction", "Discrete batch correction: combat or peptide-level median centering", "Feature-level median centering", "ComBat", "Correct batch effects: universal function", "Quality control on batch-corrected data matrix", "Heatmap of selected replicate samples", "Correlation distribution of samples", "Correlation of peptide distributions within and between proteins", "SessionInfo", "Citation", "References" ], "created": "2019-09-30 11:13:04", "modified": "2026-03-10 17:06:42", "commits": 10 }, { "source": "proBatchFeatures.Rmd", "filename": "proBatchFeatures.html", "title": "ProBatchFeatures", "author": "| Yuliya Burankova | Institute for Computational Systems Biology, University of Hamburg, Germany", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Setup", "Installation", "Loading required packages", "Loading and preparing the example dataset", "Constructing a ProBatchFeatures object", "Processing pipeline with diagnostics", "Step 1 - filtering features with too many missing values", "Step 2 - log2-transformation", "Step 3 - median normalization", "Step 4 - batch-effect correction", "Step 5 - assess processed assays", "Principal component analysis", "Hierarchical clustering", "Principal Variance Component Analysis (PVCA)", "Inspecting operation log", "Extracting data matrices from pbf object", "Session info", "Citation", "References" ], "created": "2025-09-28 17:16:39", "modified": "2026-03-10 17:06:42", "commits": 12 } ], "_score": 6.551937695364837, "_indexed": true, "_nocasepkg": "probatch", "_universes": [ "bioc", "freddsle" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.1.0", "date": "2026-05-30T07:14:34.000Z", "distro": "noble", "commit": "d27d5f9af326270032ade3e5c1d5e65adb139f48", "fileid": "a8d07676f45b1b90f17c06a7fa2df34a2a776b5bcf7f2df52dfb409ee70f83f0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677561944" }, { "r": "4.6.0", "os": "linux", "version": "2.1.0", "date": "2026-05-30T07:14:44.000Z", "distro": "noble", "commit": "d27d5f9af326270032ade3e5c1d5e65adb139f48", "fileid": "b1f069a9401b61b42a59ee4aee48fd642c68fcec7d22a4308600e5be57b6b62d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677561944" }, { "r": "4.5.3", "os": "mac", "version": "2.1.0", "date": "2026-05-30T09:42:59.000Z", "commit": "d27d5f9af326270032ade3e5c1d5e65adb139f48", "fileid": "b0ea64f5c45791e225f2c459f977cac90401c6224ed0cb0fa9aaea0d21387040", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677561944" }, { "r": "4.6.0", "os": "mac", "version": "2.1.0", "date": "2026-05-30T09:44:47.000Z", "commit": "d27d5f9af326270032ade3e5c1d5e65adb139f48", "fileid": "0c26fecc8d9c966b7396245fc2e76419e7326d75cc8f2b740e906274db6fbc7c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677561944" }, { "r": "4.6.0", "os": "wasm", "version": "2.1.0", "date": "2026-05-30T07:13:53.000Z", "commit": "d27d5f9af326270032ade3e5c1d5e65adb139f48", "fileid": "7839bd4f1e9769c20e9d6ad62b27df9cb978cef6655d8b7fe92e4c106e22778a", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677561944" }, { "r": "4.7.0", "os": "win", "version": "2.1.0", "date": "2026-05-30T07:11:50.000Z", "commit": "d27d5f9af326270032ade3e5c1d5e65adb139f48", "fileid": "57c00600a944b4332d9cc5cda27f803be7a0fd4bfb34a4151c18de4c2aabc76a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677561944" }, { "r": "4.5.3", "os": "win", "version": "2.1.0", "date": "2026-05-30T07:12:06.000Z", "commit": "d27d5f9af326270032ade3e5c1d5e65adb139f48", "fileid": "9a128b2807dd2da5db086a7de90e789b99168a4f060ac9945cb31b024abb95f9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677561944" }, { "r": "4.6.0", "os": "win", "version": "2.1.0", "date": "2026-05-30T07:11:52.000Z", "commit": "d27d5f9af326270032ade3e5c1d5e65adb139f48", "fileid": "88daedda97bdf0d0796269b88f458c0c9df6b0a7588857c5a57e6d0186c7f9e8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677561944" } ] }