├── .gitignore ├── PLSDAbatch_workflow ├── 01-supp_batch_effects_managment.Rmd ├── 02-simulation_study_Gaussian.Rmd ├── 03-simulation_study_negative_binomial.Rmd ├── 04-references.Rmd ├── GeneratedData │ ├── ADselected_50_splsda.txt │ └── HFHSselected_50_splsda.txt ├── SimulationData │ ├── balanced_Gaussian_2batches.rda │ ├── balanced_mnegbinom_2batches.rda │ ├── balanced_mnegbinom_3batches.rda │ ├── unbalanced_Gaussian_2batches.rda │ ├── unbalanced_mnegbinom_2batches.rda │ └── unbalanced_mnegbinom_3batches.rda ├── _bookdown.yml ├── _bookdown_files │ └── PLSDAbatch_workflow_files │ │ ├── figure-html │ │ ├── ADalignment-1.png │ │ ├── ADboxBefore-1.png │ │ ├── ADdensityBefore-1.png │ │ ├── ADheatmap-1.png │ │ ├── ADlm-1.png │ │ ├── ADpca-1.png │ │ ├── ADpcaBefore-1.png │ │ ├── ADprda-1.png │ │ ├── ADr21-1.png │ │ ├── ADr22-1.png │ │ ├── ADupsetR-1.png │ │ ├── HDheatmap-1.png │ │ ├── HDlmm-1.png │ │ ├── HDlmmS-1.png │ │ ├── HDpcaBefore-1.png │ │ ├── HFHSalignment-1.png │ │ ├── HFHSheatmapS-1.png │ │ ├── HFHSlm-1.png │ │ ├── HFHSlmm-1.png │ │ ├── HFHSpca-1.png │ │ ├── HFHSpcaBefore1-1.png │ │ ├── HFHSpcaBefore2-1.png │ │ ├── HFHSpcaBeforeNew1-1.png │ │ ├── HFHSpcaBeforeNew2-1.png │ │ ├── HFHSprda-1.png │ │ ├── HFHSprdaSup-1.png │ │ ├── HFHSr21-1.png │ │ ├── HFHSr22-1.png │ │ ├── HFHSupsetR-1.png │ │ ├── Spongealignment-1.png │ │ ├── Spongeheatmap-1.png │ │ ├── Spongelm-1.png │ │ ├── Spongepca-1.png │ │ ├── SpongepcaBefore-1.png │ │ ├── Spongeprda-1.png │ │ ├── Sponger21-1.png │ │ ├── Sponger22-1.png │ │ ├── SpongeupsetR-1.png │ │ ├── unnamed-chunk-100-1.png │ │ ├── unnamed-chunk-105-1.png │ │ ├── unnamed-chunk-106-1.png │ │ ├── unnamed-chunk-111-1.png │ │ ├── unnamed-chunk-112-1.png │ │ ├── unnamed-chunk-113-1.png │ │ ├── unnamed-chunk-118-1.png │ │ ├── unnamed-chunk-119-1.png │ │ ├── unnamed-chunk-120-1.png │ │ ├── unnamed-chunk-125-1.png │ │ ├── unnamed-chunk-126-1.png │ │ ├── unnamed-chunk-127-1.png │ │ ├── unnamed-chunk-132-1.png │ │ ├── unnamed-chunk-133-1.png │ │ ├── unnamed-chunk-134-1.png │ │ ├── unnamed-chunk-36-1.png │ │ ├── unnamed-chunk-36-2.png │ │ ├── unnamed-chunk-36-3.png │ │ ├── unnamed-chunk-36-4.png │ │ ├── unnamed-chunk-36-5.png │ │ ├── unnamed-chunk-36-6.png │ │ ├── unnamed-chunk-36-7.png │ │ ├── unnamed-chunk-58-1.png │ │ ├── unnamed-chunk-58-2.png │ │ ├── unnamed-chunk-58-3.png │ │ ├── unnamed-chunk-58-4.png │ │ ├── unnamed-chunk-58-5.png │ │ ├── unnamed-chunk-58-6.png │ │ ├── unnamed-chunk-89-1.png │ │ ├── unnamed-chunk-89-2.png │ │ ├── unnamed-chunk-89-3.png │ │ ├── unnamed-chunk-89-4.png │ │ ├── unnamed-chunk-89-5.png │ │ ├── unnamed-chunk-89-6.png │ │ ├── unnamed-chunk-89-7.png │ │ └── unnamed-chunk-99-1.png │ │ └── figure-latex │ │ ├── ADalignment-1.pdf │ │ ├── ADboxBefore-1.pdf │ │ ├── ADdensityBefore-1.pdf │ │ ├── ADheatmap-1.pdf │ │ ├── ADlm-1.pdf │ │ ├── ADpca-1.pdf │ │ ├── ADpcaBefore-1.pdf │ │ ├── ADprda-1.pdf │ │ ├── ADr21-1.pdf │ │ ├── ADr22-1.pdf │ │ ├── ADupsetR-1.pdf │ │ ├── HDheatmap-1.pdf │ │ ├── HDlmm-1.pdf │ │ ├── HDlmmS-1.pdf │ │ ├── HDpcaBefore-1.pdf │ │ ├── HFHSalignment-1.pdf │ │ ├── HFHSheatmapS-1.pdf │ │ ├── HFHSlm-1.pdf │ │ ├── HFHSlmm-1.pdf │ │ ├── HFHSpca-1.pdf │ │ ├── HFHSpcaBefore1-1.pdf │ │ ├── HFHSpcaBefore2-1.pdf │ │ ├── HFHSpcaBeforeNew1-1.pdf │ │ ├── HFHSpcaBeforeNew2-1.pdf │ │ ├── HFHSprda-1.pdf │ │ ├── HFHSprdaSup-1.pdf │ │ ├── HFHSr21-1.pdf │ │ ├── HFHSr22-1.pdf │ │ ├── HFHSupsetR-1.pdf │ │ ├── Spongealignment-1.pdf │ │ ├── Spongeheatmap-1.pdf │ │ ├── Spongelm-1.pdf │ │ ├── Spongepca-1.pdf │ │ ├── SpongepcaBefore-1.pdf │ │ ├── Spongeprda-1.pdf │ │ ├── Sponger21-1.pdf │ │ ├── Sponger22-1.pdf │ │ ├── SpongeupsetR-1.pdf │ │ ├── unnamed-chunk-100-1.pdf │ │ ├── unnamed-chunk-105-1.pdf │ │ ├── unnamed-chunk-106-1.pdf │ │ ├── unnamed-chunk-111-1.pdf │ │ ├── unnamed-chunk-112-1.pdf │ │ ├── unnamed-chunk-113-1.pdf │ │ ├── unnamed-chunk-118-1.pdf │ │ ├── unnamed-chunk-119-1.pdf │ │ ├── unnamed-chunk-120-1.pdf │ │ ├── unnamed-chunk-125-1.pdf │ │ ├── unnamed-chunk-126-1.pdf │ │ ├── unnamed-chunk-127-1.pdf │ │ ├── unnamed-chunk-132-1.pdf │ │ ├── unnamed-chunk-133-1.pdf │ │ ├── unnamed-chunk-134-1.pdf │ │ ├── unnamed-chunk-36-1.pdf │ │ ├── unnamed-chunk-36-2.pdf │ │ ├── unnamed-chunk-36-3.pdf │ │ ├── unnamed-chunk-36-4.pdf │ │ ├── unnamed-chunk-36-5.pdf │ │ ├── unnamed-chunk-36-6.pdf │ │ ├── unnamed-chunk-36-7.pdf │ │ ├── unnamed-chunk-58-1.pdf │ │ ├── unnamed-chunk-58-2.pdf │ │ ├── unnamed-chunk-58-3.pdf │ │ ├── unnamed-chunk-58-4.pdf │ │ ├── unnamed-chunk-58-5.pdf │ │ ├── unnamed-chunk-58-6.pdf │ │ ├── unnamed-chunk-89-1.pdf │ │ ├── unnamed-chunk-89-2.pdf │ │ ├── unnamed-chunk-89-3.pdf │ │ ├── unnamed-chunk-89-4.pdf │ │ ├── unnamed-chunk-89-5.pdf │ │ ├── unnamed-chunk-89-6.pdf │ │ ├── unnamed-chunk-89-7.pdf │ │ └── unnamed-chunk-99-1.pdf ├── _output.yml ├── agis-logo.png ├── book.bib ├── built_in_functions │ └── data_simulation.R ├── data │ ├── HD_data.rda │ └── HFHS_data.rda ├── figures │ ├── data_description.png │ └── function_description.png ├── index.Rmd ├── packages.bib ├── preamble.tex └── style.css ├── README.md └── docs ├── 404.html ├── PLSDAbatch_workflow.epub ├── PLSDAbatch_workflow.pdf ├── PLSDAbatch_workflow.tex ├── PLSDAbatch_workflow_files └── figure-html │ ├── ADalignment-1.png │ ├── ADboxBefore-1.png │ ├── ADdensityBefore-1.png │ ├── ADheatmap-1.png │ ├── ADlm-1.png │ ├── ADpca-1.png │ ├── ADpcaBefore-1.png │ ├── ADprda-1.png │ ├── ADr21-1.png │ ├── ADr22-1.png │ ├── ADupsetR-1.png │ ├── HDheatmap-1.png │ ├── HDlmm-1.png │ ├── HDlmmS-1.png │ ├── HDpcaBefore-1.png │ ├── HFHSalignment-1.png │ ├── HFHSheatmapS-1.png │ ├── HFHSlm-1.png │ ├── HFHSlmm-1.png │ ├── HFHSpca-1.png │ ├── HFHSpcaBefore1-1.png │ ├── HFHSpcaBefore2-1.png │ ├── HFHSpcaBeforeNew1-1.png │ ├── HFHSpcaBeforeNew2-1.png │ ├── HFHSprda-1.png │ ├── HFHSprdaSup-1.png │ ├── HFHSr21-1.png │ ├── HFHSr22-1.png │ ├── HFHSupsetR-1.png │ ├── Spongealignment-1.png │ ├── Spongeheatmap-1.png │ ├── Spongelm-1.png │ ├── Spongepca-1.png │ ├── SpongepcaBefore-1.png │ ├── Spongeprda-1.png │ ├── Sponger21-1.png │ ├── Sponger22-1.png │ ├── SpongeupsetR-1.png │ ├── unnamed-chunk-100-1.png │ ├── unnamed-chunk-105-1.png │ ├── unnamed-chunk-106-1.png │ ├── unnamed-chunk-111-1.png │ ├── unnamed-chunk-112-1.png │ ├── unnamed-chunk-113-1.png │ ├── unnamed-chunk-118-1.png │ ├── unnamed-chunk-119-1.png │ ├── unnamed-chunk-120-1.png │ ├── unnamed-chunk-125-1.png │ ├── unnamed-chunk-126-1.png │ ├── unnamed-chunk-127-1.png │ ├── unnamed-chunk-132-1.png │ ├── unnamed-chunk-133-1.png │ ├── unnamed-chunk-134-1.png │ └── unnamed-chunk-99-1.png ├── batch-effects-management-in-simulation-studies-gaussian-distribution.html ├── batch-effects-management-in-simulation-studies-negative-binomial-distribution.html ├── figures ├── data_description.png └── function_description.png ├── index.html ├── libs ├── anchor-sections-1.1.0 │ ├── anchor-sections-hash.css │ ├── anchor-sections.css │ └── anchor-sections.js ├── gitbook-2.6.7 │ ├── css │ │ ├── fontawesome │ │ │ └── fontawesome-webfont.ttf │ │ ├── plugin-bookdown.css │ │ ├── plugin-clipboard.css │ │ ├── plugin-fontsettings.css │ │ ├── plugin-highlight.css │ │ ├── plugin-search.css │ │ ├── plugin-table.css │ │ └── style.css │ └── js │ │ ├── app.min.js │ │ ├── clipboard.min.js │ │ ├── jquery.highlight.js │ │ ├── plugin-bookdown.js │ │ ├── plugin-clipboard.js │ │ ├── plugin-fontsettings.js │ │ ├── plugin-search.js │ │ └── plugin-sharing.js └── jquery-3.6.0 │ └── jquery-3.6.0.min.js ├── reference-keys.txt ├── references-4.html ├── search_index.json ├── style.css └── supplementary-materials-for-batch-effects-management-in-case-studies.html /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | 6 | ## mac 7 | .DS_Store 8 | 9 | ## 10 | PLSDAbatch_workflow/PLSDAbatch_workflow.Rproj 11 | 12 | -------------------------------------------------------------------------------- /PLSDAbatch_workflow/04-references.Rmd: -------------------------------------------------------------------------------- 1 | `r if (knitr::is_html_output()) ' 2 | # References {-} 3 | '` 4 | -------------------------------------------------------------------------------- /PLSDAbatch_workflow/GeneratedData/ADselected_50_splsda.txt: -------------------------------------------------------------------------------- 1 | $`PLSDA-batch` 2 | Kingdom Phylum Class Order 3 | OTU71 Bacteria Firmicutes Clostridia Clostridiales 4 | OTU106 Archaea Euryarchaeota Thermoplasmata Thermoplasmatales 5 | OTU84 Bacteria Firmicutes Clostridia Clostridiales 6 | OTU177 Bacteria Firmicutes Clostridia Clostridiales 7 | Family Genus 8 | OTU71 Ruminococcaceae Ruminiclostridium 9 | OTU106 Thermoplasmatales Incertae Sedis unknown genus 10 | OTU84 Ruminococcaceae Acetanaerobacterium 11 | OTU177 Christensenellaceae Christensenellaceae R-7 group 12 | Species 13 | OTU71 unknown species 14 | OTU106 unknown species 15 | OTU84 unknown species 16 | OTU177 unknown species 17 | 18 | $`sPLSDA-batch` 19 | Kingdom Phylum Class Order 20 | OTU116 Bacteria Firmicutes Clostridia Clostridiales 21 | OTU209 Bacteria Firmicutes Clostridia Clostridiales 22 | OTU216 Bacteria Firmicutes Clostridia Clostridiales 23 | OTU87 Bacteria Firmicutes Clostridia Clostridiales 24 | Family Genus Species 25 | OTU116 Clostridiales vadinBB60 group unknown genus unknown species 26 | OTU209 Peptococcaceae Sporotomaculum Sporotomaculum syntrophicum 27 | OTU216 Family XIV unknown genus unknown species 28 | OTU87 Peptococcaceae Pelotomaculum unknown species 29 | 30 | $`Before correction` 31 | Kingdom Phylum Class Order 32 | OTU110 Bacteria Firmicutes Clostridia Clostridiales 33 | OTU141 Bacteria Firmicutes Clostridia Clostridiales 34 | OTU31 Bacteria Firmicutes Bacilli Bacillales 35 | OTU86 Archaea Euryarchaeota Methanomicrobia Methanomicrobiales 36 | Family Genus Species 37 | OTU110 Lachnospiraceae Anaerosporobacter Multi-affiliation 38 | OTU141 Ruminococcaceae unknown genus unknown species 39 | OTU31 Paenibacillaceae Aneurinibacillus unknown species 40 | OTU86 Methanomicrobiaceae Methanoculleus unknown species 41 | 42 | $`Before correction:ComBat` 43 | Kingdom Phylum Class Order Family 44 | OTU218 Bacteria Firmicutes Clostridia Clostridiales Christensenellaceae 45 | Genus Species 46 | OTU218 Christensenellaceae R-7 group unknown species 47 | 48 | $`PLSDA-batch:sPLSDA-batch` 49 | Kingdom Phylum Class Order Family 50 | OTU225 Bacteria Bacteroidetes Bacteroidia Bacteroidales Marinilabiaceae 51 | OTU17 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae 52 | Genus Species 53 | OTU225 unknown genus unknown species 54 | OTU17 Acetivibrio Multi-affiliation 55 | 56 | $`removeBatchEffect:ComBat` 57 | Kingdom Phylum Class Order Family 58 | OTU91 Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae 59 | OTU16 Bacteria Synergistetes Synergistia Synergistales Synergistaceae 60 | OTU85 Bacteria Synergistetes Synergistia Synergistales Synergistaceae 61 | OTU18 Bacteria Firmicutes Clostridia Clostridiales Christensenellaceae 62 | Genus Species 63 | OTU91 unknown genus unknown species 64 | OTU16 unknown genus unknown species 65 | OTU85 unknown genus Multi-affiliation 66 | OTU18 unknown genus unknown species 67 | 68 | $`Before correction:PLSDA-batch` 69 | Kingdom Phylum Class Order Family 70 | OTU223 Bacteria Chloroflexi Anaerolineae Anaerolineales Anaerolineaceae 71 | Genus Species 72 | OTU223 unknown genus anaerobic digester metagenome 73 | 74 | $`Before correction:removeBatchEffect` 75 | Kingdom Phylum Class Order Family 76 | OTU143 Bacteria Spirochaetae Spirochaetes Spirochaetales Spirochaetaceae 77 | OTU211 Bacteria Synergistetes Synergistia Synergistales Synergistaceae 78 | Genus Species 79 | OTU143 Sphaerochaeta unknown species 80 | OTU211 Aminobacterium Aminobacterium colombiense 81 | 82 | $`Before correction:ComBat:PLSDA-batch` 83 | Kingdom Phylum Class Order Family 84 | OTU159 Bacteria Chloroflexi Anaerolineae Anaerolineales Anaerolineaceae 85 | Genus Species 86 | OTU159 unknown genus unknown species 87 | 88 | $`Before correction:PLSDA-batch:sPLSDA-batch` 89 | Kingdom Phylum Class Order Family 90 | OTU105 Bacteria Firmicutes Clostridia Clostridiales Syntrophomonadaceae 91 | Genus Species 92 | OTU105 Syntrophomonas anaerobic digester metagenome 93 | 94 | $`removeBatchEffect:ComBat:PLSDA-batch:sPLSDA-batch` 95 | Kingdom Phylum Class Order Family 96 | OTU19 Bacteria Firmicutes Clostridia Clostridiales Family XIV 97 | OTU41 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae 98 | OTU9 Bacteria Firmicutes Clostridia Clostridiales Christensenellaceae 99 | OTU27 Bacteria Firmicutes Clostridia Clostridiales Christensenellaceae 100 | Genus Species 101 | OTU19 unknown genus unknown species 102 | OTU41 unknown genus unknown species 103 | OTU9 Christensenellaceae R-7 group unknown species 104 | OTU27 unknown genus unknown species 105 | 106 | $`Before correction:removeBatchEffect:ComBat:PLSDA-batch` 107 | Kingdom Phylum Class Order Family Genus 108 | OTU117 Bacteria Firmicutes Clostridia B55-F-B-G02 unknown family unknown genus 109 | Species 110 | OTU117 unknown species 111 | 112 | $`Before correction:removeBatchEffect:ComBat:sPLSDA-batch` 113 | Kingdom Phylum Class Order 114 | OTU130 Bacteria Firmicutes Bacilli TSCOR001-H18 115 | OTU145 Bacteria Proteobacteria Deltaproteobacteria Bdellovibrionales 116 | OTU44 Bacteria Planctomycetes Phycisphaerae KCLunmb-38-53 117 | Family Genus Species 118 | OTU130 unknown family unknown genus unknown species 119 | OTU145 Bacteriovoracaceae unknown genus unknown species 120 | OTU44 unknown family unknown genus unknown species 121 | 122 | $`Before correction:removeBatchEffect:ComBat:PLSDA-batch:sPLSDA-batch` 123 | Kingdom Phylum Class Order 124 | OTU46 Bacteria Firmicutes Clostridia Clostridiales 125 | OTU24 Bacteria Firmicutes Clostridia Clostridiales 126 | OTU68 Bacteria Firmicutes Clostridia Clostridiales 127 | OTU59 Bacteria Firmicutes Clostridia Thermoanaerobacterales 128 | OTU28 Bacteria Firmicutes Clostridia Clostridiales 129 | OTU104 Bacteria Firmicutes Clostridia Clostridiales 130 | OTU61 Bacteria Firmicutes Clostridia Clostridiales 131 | OTU35 Bacteria Firmicutes Clostridia Clostridiales 132 | OTU118 Bacteria Firmicutes Clostridia M55-D21 133 | OTU65 Bacteria Firmicutes Clostridia Thermoanaerobacterales 134 | OTU193 Bacteria Firmicutes Clostridia Clostridiales 135 | OTU54 Bacteria Firmicutes Erysipelotrichia Erysipelotrichales 136 | OTU96 Bacteria Firmicutes Clostridia MBA03 137 | OTU88 Bacteria Firmicutes Clostridia Clostridiales 138 | OTU43 Bacteria Firmicutes Clostridia Clostridiales 139 | OTU6 Bacteria Firmicutes Clostridia Clostridiales 140 | OTU62 Bacteria Firmicutes Clostridia Clostridiales 141 | OTU56 Bacteria Firmicutes Clostridia Clostridiales 142 | OTU198 Bacteria Bacteroidetes Bacteroidia Bacteroidales 143 | OTU144 Bacteria Firmicutes Clostridia Clostridiales 144 | OTU23 Bacteria Proteobacteria Deltaproteobacteria Bdellovibrionales 145 | OTU48 Bacteria Firmicutes Clostridia Clostridiales 146 | OTU135 Bacteria Bacteroidetes Bacteroidia Bacteroidales 147 | OTU51 Bacteria Chloroflexi Anaerolineae Anaerolineales 148 | OTU74 Bacteria Firmicutes Clostridia Clostridiales 149 | OTU138 Bacteria Firmicutes Clostridia Clostridiales 150 | OTU205 Bacteria Firmicutes Clostridia Clostridiales 151 | OTU7 Bacteria Bacteroidetes Bacteroidia Bacteroidales 152 | OTU36 Bacteria Firmicutes Clostridia Clostridiales 153 | OTU127 Bacteria Firmicutes Clostridia Clostridiales 154 | OTU151 Bacteria Firmicutes Clostridia Clostridiales 155 | OTU5 Bacteria Bacteroidetes Bacteroidia Bacteroidales 156 | OTU64 Bacteria Firmicutes Clostridia Clostridiales 157 | OTU94 Bacteria Firmicutes Clostridia Clostridiales 158 | OTU76 Bacteria Armatimonadetes Chthonomonadetes Chthonomonadales 159 | OTU248 Bacteria Bacteroidetes Bacteroidia Bacteroidales 160 | Family Genus 161 | OTU46 Ruminococcaceae Ruminiclostridium 162 | OTU24 Gracilibacteraceae Lutispora 163 | OTU68 Family XIV unknown genus 164 | OTU59 Thermoanaerobacteraceae Moorella 165 | OTU28 Heliobacteriaceae Hydrogenispora 166 | OTU104 Peptococcaceae Pelotomaculum 167 | OTU61 Gracilibacteraceae Multi-affiliation 168 | OTU35 Syntrophomonadaceae Syntrophomonas 169 | OTU118 unknown family unknown genus 170 | OTU65 SRB2 unknown genus 171 | OTU193 Lachnospiraceae Tyzzerella 172 | OTU54 Erysipelotrichaceae Erysipelotrichaceae UCG-004 173 | OTU96 unknown family unknown genus 174 | OTU88 Caldicoprobacteraceae Caldicoprobacter 175 | OTU43 Ruminococcaceae Ruminiclostridium 176 | OTU6 Lachnospiraceae Mobilitalea 177 | OTU62 Clostridiales vadinBB60 group unknown genus 178 | OTU56 Christensenellaceae Christensenellaceae R-7 group 179 | OTU198 Marinilabiaceae Ruminofilibacter 180 | OTU144 Clostridiales vadinBB60 group unknown genus 181 | OTU23 Bacteriovoracaceae unknown genus 182 | OTU48 Lachnospiraceae Anaerosporobacter 183 | OTU135 Porphyromonadaceae Proteiniphilum 184 | OTU51 Anaerolineaceae unknown genus 185 | OTU74 Lachnospiraceae unknown genus 186 | OTU138 Ruminococcaceae Ruminiclostridium 187 | OTU205 Christensenellaceae unknown genus 188 | OTU7 Rikenellaceae Blvii28 wastewater-sludge group 189 | OTU36 Family XIV unknown genus 190 | OTU127 Clostridiales Incertae Sedis Proteiniborus 191 | OTU151 Christensenellaceae Christensenellaceae R-7 group 192 | OTU5 Marinilabiaceae Ruminofilibacter 193 | OTU64 Gracilibacteraceae Multi-affiliation 194 | OTU94 Ruminococcaceae Ruminococcus 1 195 | OTU76 unknown family unknown genus 196 | OTU248 Marinilabiaceae Ruminofilibacter 197 | Species 198 | OTU46 unknown species 199 | OTU24 unknown species 200 | OTU68 unknown species 201 | OTU59 Multi-affiliation 202 | OTU28 unknown species 203 | OTU104 Multi-affiliation 204 | OTU61 Multi-affiliation 205 | OTU35 unknown species 206 | OTU118 unknown species 207 | OTU65 unknown species 208 | OTU193 unknown species 209 | OTU54 unknown species 210 | OTU96 unknown species 211 | OTU88 unknown species 212 | OTU43 unknown species 213 | OTU6 unknown species 214 | OTU62 unknown species 215 | OTU56 unknown species 216 | OTU198 Multi-affiliation 217 | OTU144 unknown species 218 | OTU23 unknown species 219 | OTU48 unknown species 220 | OTU135 Multi-affiliation 221 | OTU51 unknown species 222 | OTU74 unknown species 223 | OTU138 unknown species 224 | OTU205 unknown species 225 | OTU7 unknown species 226 | OTU36 unknown species 227 | OTU127 Multi-affiliation 228 | OTU151 unknown species 229 | OTU5 Multi-affiliation 230 | OTU64 Multi-affiliation 231 | OTU94 bacterium enrichment culture clone KWE55-24 232 | OTU76 unknown species 233 | OTU248 Multi-affiliation 234 | 235 | -------------------------------------------------------------------------------- /PLSDAbatch_workflow/GeneratedData/HFHSselected_50_splsda.txt: -------------------------------------------------------------------------------- 1 | $`PLSDA-batch` 2 | HFHS_data$FullData$taxa[x, ] 3 | Kingdom Bacteria 4 | Phylum Firmicutes 5 | Class Clostridia 6 | Order Clostridiales 7 | Family 8 | Genus 9 | Species 10 | 11 | $`Before correction` 12 | Kingdom Phylum Class Order Family 13 | 327808 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae 14 | 338796 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae 15 | Genus Species 16 | 327808 Oscillospira 17 | 338796 Oscillospira 18 | 19 | $`PLSDA-batch:RUVIII` 20 | HFHS_data$FullData$taxa[x, ] 21 | Kingdom Bacteria 22 | Phylum Firmicutes 23 | Class Clostridia 24 | Order Clostridiales 25 | Family 26 | Genus 27 | Species 28 | 29 | $`ComBat:PLSDA-batch:RUVIII` 30 | Kingdom Phylum Class Order 31 | 186332 Bacteria Firmicutes Clostridia Clostridiales 32 | 262095 Bacteria Firmicutes Erysipelotrichi Erysipelotrichales 33 | 276597 Bacteria Firmicutes Clostridia Clostridiales 34 | Family Genus Species 35 | 186332 Lachnospiraceae [Ruminococcus] gnavus 36 | 262095 Erysipelotrichaceae 37 | 276597 38 | 39 | $`Before correction:removeBatchEffect` 40 | Kingdom Phylum Class Order Family 41 | 581933 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae 42 | 206817 Bacteria Bacteroidetes Bacteroidia Bacteroidales S24-7 43 | Genus Species 44 | 581933 Oscillospira 45 | 206817 46 | 47 | $`removeBatchEffect:ComBat:PLSDA-batch` 48 | HFHS_data$FullData$taxa[x, ] 49 | Kingdom Bacteria 50 | Phylum Firmicutes 51 | Class Clostridia 52 | Order Clostridiales 53 | Family Ruminococcaceae 54 | Genus Oscillospira 55 | Species 56 | 57 | $`Before correction:removeBatchEffect:ComBat` 58 | HFHS_data$FullData$taxa[x, ] 59 | Kingdom Bacteria 60 | Phylum Firmicutes 61 | Class Clostridia 62 | Order Clostridiales 63 | Family Ruminococcaceae 64 | Genus Oscillospira 65 | Species 66 | 67 | $`Before correction:removeBatchEffect:RUVIII` 68 | HFHS_data$FullData$taxa[x, ] 69 | Kingdom Bacteria 70 | Phylum Bacteroidetes 71 | Class Bacteroidia 72 | Order Bacteroidales 73 | Family S24-7 74 | Genus 75 | Species 76 | 77 | $`removeBatchEffect:ComBat:PLSDA-batch:RUVIII` 78 | HFHS_data$FullData$taxa[x, ] 79 | Kingdom Bacteria 80 | Phylum Firmicutes 81 | Class Clostridia 82 | Order Clostridiales 83 | Family 84 | Genus 85 | Species 86 | 87 | $`Before correction:removeBatchEffect:ComBat:RUVIII` 88 | HFHS_data$FullData$taxa[x, ] 89 | Kingdom Bacteria 90 | Phylum Bacteroidetes 91 | Class Bacteroidia 92 | Order Bacteroidales 93 | Family S24-7 94 | Genus 95 | Species 96 | 97 | $`Before correction:removeBatchEffect:ComBat:PLSDA-batch` 98 | Kingdom Phylum Class Order Family 99 | 434089 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae 100 | 272953 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae 101 | 353982 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae 102 | 326940 Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae 103 | Genus Species 104 | 434089 105 | 272953 Oscillospira 106 | 353982 107 | 326940 108 | 109 | $RUVIII 110 | Kingdom Phylum Class Order Family Genus 111 | 398255 Bacteria Bacteroidetes Bacteroidia Bacteroidales S24-7 112 | 205160 Bacteria Bacteroidetes Bacteroidia Bacteroidales S24-7 113 | 384555 Bacteria Bacteroidetes Bacteroidia Bacteroidales S24-7 114 | 1107652 Bacteria Bacteroidetes Bacteroidia Bacteroidales Rikenellaceae 115 | Species 116 | 398255 117 | 205160 118 | 384555 119 | 1107652 120 | 121 | $`Before correction:removeBatchEffect:ComBat:PLSDA-batch:RUVIII` 122 | Kingdom Phylum Class Order 123 | 192222 Bacteria Bacteroidetes Bacteroidia Bacteroidales 124 | 400599 Bacteria Firmicutes Clostridia Clostridiales 125 | 315147 Bacteria Bacteroidetes Bacteroidia Bacteroidales 126 | 348038 Bacteria Bacteroidetes Bacteroidia Bacteroidales 127 | 442846 Bacteria Bacteroidetes Bacteroidia Bacteroidales 128 | 263479 Bacteria Bacteroidetes Bacteroidia Bacteroidales 129 | 175272 Bacteria Bacteroidetes Bacteroidia Bacteroidales 130 | 265322 Bacteria Bacteroidetes Bacteroidia Bacteroidales 131 | 331043 Bacteria Bacteroidetes Bacteroidia Bacteroidales 132 | 339905 Bacteria Bacteroidetes Bacteroidia Bacteroidales 133 | 401384 Bacteria Firmicutes Clostridia Clostridiales 134 | 197644 Bacteria Bacteroidetes Bacteroidia Bacteroidales 135 | 348821 Bacteria Bacteroidetes Bacteroidia Bacteroidales 136 | 198339 Bacteria Bacteroidetes Bacteroidia Bacteroidales 137 | 275218 Bacteria Firmicutes Clostridia Clostridiales 138 | 315430 Bacteria Bacteroidetes Bacteroidia Bacteroidales 139 | 174590 Bacteria Bacteroidetes Bacteroidia Bacteroidales 140 | 184381 Bacteria Bacteroidetes Bacteroidia Bacteroidales 141 | 4378740 Bacteria Bacteroidetes Bacteroidia Bacteroidales 142 | 462764 Bacteria Firmicutes Clostridia Clostridiales 143 | 275476 Bacteria Firmicutes Clostridia Clostridiales 144 | 295564 Bacteria Bacteroidetes Bacteroidia Bacteroidales 145 | 349798 Bacteria Firmicutes Clostridia Clostridiales 146 | 177917 Bacteria Bacteroidetes Bacteroidia Bacteroidales 147 | 177512 Bacteria Bacteroidetes Bacteroidia Bacteroidales 148 | 199118 Bacteria Bacteroidetes Bacteroidia Bacteroidales 149 | 4481506 Bacteria Bacteroidetes Bacteroidia Bacteroidales 150 | 2897325 Bacteria Proteobacteria Deltaproteobacteria Desulfovibrionales 151 | 312440 Bacteria Bacteroidetes Bacteroidia Bacteroidales 152 | 355746 Bacteria Bacteroidetes Bacteroidia Bacteroidales 153 | 196733 Bacteria Bacteroidetes Bacteroidia Bacteroidales 154 | 196672 Bacteria Bacteroidetes Bacteroidia Bacteroidales 155 | 267335 Bacteria Firmicutes Clostridia Clostridiales 156 | 212201 Bacteria Bacteroidetes Bacteroidia Bacteroidales 157 | 272213 Bacteria Firmicutes Clostridia Clostridiales 158 | 1108745 Bacteria Firmicutes Clostridia Clostridiales 159 | 198753 Bacteria Firmicutes Clostridia Clostridiales 160 | 351309 Bacteria Firmicutes Clostridia Clostridiales 161 | 321484 Bacteria Firmicutes Clostridia Clostridiales 162 | Family Genus Species 163 | 192222 Prevotellaceae 164 | 400599 165 | 315147 S24-7 166 | 348038 S24-7 167 | 442846 S24-7 168 | 263479 S24-7 169 | 175272 S24-7 170 | 265322 S24-7 171 | 331043 S24-7 172 | 339905 S24-7 173 | 401384 Ruminococcaceae Oscillospira 174 | 197644 S24-7 175 | 348821 S24-7 176 | 198339 S24-7 177 | 275218 Ruminococcaceae 178 | 315430 S24-7 179 | 174590 S24-7 180 | 184381 S24-7 181 | 4378740 Prevotellaceae Prevotella 182 | 462764 Ruminococcaceae Ruminococcus 183 | 275476 Ruminococcaceae Oscillospira 184 | 295564 S24-7 185 | 349798 Ruminococcaceae Oscillospira 186 | 177917 S24-7 187 | 177512 S24-7 188 | 199118 S24-7 189 | 4481506 S24-7 190 | 2897325 Desulfovibrionaceae Bilophila 191 | 312440 S24-7 192 | 355746 S24-7 193 | 196733 S24-7 194 | 196672 S24-7 195 | 267335 Lachnospiraceae [Ruminococcus] gnavus 196 | 212201 S24-7 197 | 272213 Ruminococcaceae 198 | 1108745 [Mogibacteriaceae] 199 | 198753 Ruminococcaceae 200 | 351309 201 | 321484 Ruminococcaceae Oscillospira 202 | 203 | -------------------------------------------------------------------------------- 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