23 Partial least square analysis
23.1 Prepare the data
library(ropls)
data(sacurine)
names(sacurine)## [1] "dataMatrix" "sampleMetadata" "variableMetadata"We attach sacurine to the search path and display a summary of the content of the dataMatrix, sampleMetadata and variableMetadata with the strF Function of the ropls package (see also str):
attach(sacurine)
strF(dataMatrix)## dim class mode typeof size NAs min mean median max
## 183 x 109 matrix numeric double 0.2 Mb 0 -0.3 4.2 4.3 6
## (2-methoxyethoxy)propanoic acid isomer (gamma)Glu-Leu/Ile ...
## HU_011 3.019766011 3.888479324 ...
## HU_014 3.81433889 4.277148905 ...
## ... ... ... ...
## HU_208 3.748127215 4.523763202 ...
## HU_209 4.208859398 4.675880567 ...
## Valerylglycine isomer 2 Xanthosine
## HU_011 3.889078716 4.075879575
## HU_014 4.181765852 4.195761901
## ... ... ...
## HU_208 4.634338821 4.487781609
## HU_209 4.47194762 4.222953354head(dataMatrix)## (2-methoxyethoxy)propanoic acid isomer (gamma)Glu-Leu/Ile
## HU_011 3.019766 3.888479
## HU_014 3.814339 4.277149
## HU_015 3.519691 4.195649
## HU_017 2.562183 4.323760
## HU_018 3.781922 4.629329
## HU_019 4.161074 4.412266
## 1-Methyluric acid 1-Methylxanthine 1,3-Dimethyluric acid
## HU_011 3.869006 3.717259 3.535461
## HU_014 3.837704 3.776851 3.932581
## HU_015 4.102254 4.291665 3.955376
## HU_017 4.538520 4.432216 4.228491
## HU_018 4.178829 4.117360 4.005545
## HU_019 4.516805 4.562052 4.320582
## 1,7-Dimethyluric acid 2-acetamido-4-methylphenyl acetate
## HU_011 3.325199 4.204754
## HU_014 4.025125 5.181858
## HU_015 3.972904 3.885680
## HU_017 4.109927 4.237915
## HU_018 4.024092 1.852994
## HU_019 4.326856 4.080681
## 2-Aminoadipic acid 2-Hydroxybenzyl alcohol 2-Isopropylmalic acid
## HU_011 4.080204 4.560049 3.466916
## HU_014 4.359246 3.158212 3.942746
## HU_015 4.249111 4.290525 3.539600
## HU_017 4.231404 3.644976 3.152084
## HU_018 4.323679 4.095923 4.490116
## HU_019 4.244485 4.428005 4.156567
## 2-Methylhippuric acid 2,2-Dimethylglutaric acid
## HU_011 4.297716 3.799720
## HU_014 3.833793 4.192342
## HU_015 4.199262 4.146924
## HU_017 3.865260 4.233270
## HU_018 4.271223 4.755177
## HU_019 3.831930 4.333599
## 3-Hydroxybenzyl alcohol 3-Hydroxyphenylacetic acid
## HU_011 3.502958 4.672721
## HU_014 4.370053 4.490127
## HU_015 3.990814 4.416155
## HU_017 4.151260 3.960912
## HU_018 4.373425 4.247532
## HU_019 1.446237 4.164327
## 3-Indole carboxylic acid glucuronide 3-Methyl-2-oxovaleric acid
## HU_011 3.548979 3.956110
## HU_014 4.344955 4.062870
## HU_015 4.174503 4.420565
## HU_017 4.688053 4.146152
## HU_018 3.276676 4.351114
## HU_019 4.206905 4.341494
## 3-Methylcrotonylglycine 3,3-Dimethylglutaric acid
## HU_011 4.204465 4.223994
## HU_014 4.055144 4.486961
## HU_015 4.148095 4.137063
## HU_017 4.193130 4.200239
## HU_018 4.225720 4.569052
## HU_019 4.127074 4.195226
## 3,4-Dihydroxybenzeneacetic acid
## HU_011 3.400454
## HU_014 4.366695
## HU_015 3.965742
## HU_017 4.121298
## HU_018 4.373747
## HU_019 2.320550
## 3,5-dihydroxybenzoic acid/3,4-dihydroxybenzoic acid
## HU_011 4.494138
## HU_014 4.118021
## HU_015 4.284274
## HU_017 4.118248
## HU_018 4.077463
## HU_019 4.107163
## 3,7-Dimethyluric acid 4-Acetamidobutanoic acid isomer 2
## HU_011 4.233820 4.046984
## HU_014 3.596651 4.218431
## HU_015 3.954022 3.995719
## HU_017 3.995039 4.006450
## HU_018 3.908515 4.564357
## HU_019 4.720603 4.193068
## 4-Acetamidobutanoic acid isomer 3 4-Hydroxybenzoic acid
## HU_011 3.964380 4.581811
## HU_014 4.087865 4.675483
## HU_015 4.031485 4.248248
## HU_017 3.884681 4.171788
## HU_018 4.347509 4.660293
## HU_019 4.040541 4.335561
## 4-Methylhippuric acid/3-Methylhippuric acid
## HU_011 3.242186
## HU_014 3.838007
## HU_015 4.723900
## HU_017 3.617350
## HU_018 4.285848
## HU_019 3.430342
## 5-Hydroxyindoleacetic acid 5-Sulfosalicylic acid
## HU_011 4.307545 4.023477
## HU_014 4.402027 4.083692
## HU_015 3.975413 4.232119
## HU_017 4.168655 3.088972
## HU_018 4.502182 4.142686
## HU_019 4.281092 3.950241
## 6-(2-hydroxyethoxy)-6-oxohexanoic acid
## HU_011 3.758640
## HU_014 4.329163
## HU_015 3.994170
## HU_017 4.436174
## HU_018 4.442814
## HU_019 4.260599
## 6-(carboxymethoxy)-hexanoic acid 9-Methylxanthine
## HU_011 3.445392 4.403909
## HU_014 3.999589 4.211293
## HU_015 4.039267 4.073960
## HU_017 4.084428 4.257367
## HU_018 4.527800 3.662754
## HU_019 4.114818 4.262501
## Acetaminophen glucuronide Acetylphenylalanine
## HU_011 1.64620136 4.169514
## HU_014 0.09467123 4.515993
## HU_015 -0.15947672 4.083460
## HU_017 0.32143853 3.767910
## HU_018 1.76127463 4.187942
## HU_019 4.62568088 4.292496
## alpha-N-Phenylacetyl-glutamine Aminosalicyluric acid
## HU_011 4.406638 4.125306
## HU_014 4.362682 3.942512
## HU_015 4.101540 4.004895
## HU_017 4.173137 4.277246
## HU_018 4.332330 4.307816
## HU_019 4.366653 3.908610
## Asp-Leu/Ile isomer 1 Asp-Leu/Ile isomer 2 Aspartic acid
## HU_011 3.565669 3.706871 4.262679
## HU_014 3.852859 3.624547 4.278906
## HU_015 3.879881 3.965623 4.225658
## HU_017 3.564683 4.000451 4.476138
## HU_018 4.710114 4.414012 4.460986
## HU_019 4.551170 4.417869 4.545151
## Azelaic acid Benzoic acid isomer Chenodeoxycholic acid isomer
## HU_011 4.419660 3.867245 3.507941
## HU_014 4.331720 4.830236 3.925771
## HU_015 4.105070 3.371990 4.765679
## HU_017 4.017999 3.724525 4.058410
## HU_018 4.320763 4.593359 4.379709
## HU_019 4.641622 4.475130 4.120224
## Cinnamoylglycine Citric acid Dehydroepiandrosterone 3-glucuronide
## HU_011 3.981493 4.077505 4.276799
## HU_014 3.381453 4.418117 3.781079
## HU_015 3.773393 4.179830 4.039523
## HU_017 4.213982 4.218916 3.960037
## HU_018 2.636678 4.294479 4.178258
## HU_019 4.071694 4.386380 4.018968
## Dehydroepiandrosterone sulfate Deoxyhexose Dimethylguanosine
## HU_011 4.462774 3.760569 4.052598
## HU_014 3.806104 3.809186 4.269907
## HU_015 3.193502 4.226145 4.197532
## HU_017 4.165680 3.997357 4.350023
## HU_018 4.363253 4.084736 4.408429
## HU_019 3.986997 4.296965 4.310144
## FMNH2 Fumaric acid Gentisic acid Glu-Val
## HU_011 3.565083 3.567561 4.300974 3.706666
## HU_014 4.208395 3.840097 4.584677 4.310927
## HU_015 4.034409 4.384064 4.764176 4.289509
## HU_017 4.233037 3.416630 4.062663 4.376818
## HU_018 4.597364 4.091964 4.431808 4.721889
## HU_019 4.199745 4.012107 4.238883 4.392128
## Gluconic acid and/or isomers Glucuronic acid and/or isomers
## HU_011 4.288424 4.271366
## HU_014 4.586464 4.701159
## HU_015 4.096407 4.123025
## HU_017 4.743170 4.593438
## HU_018 4.614798 4.461186
## HU_019 4.334139 4.461209
## Glyceric acid Glycocholic acid isomer 2 Glycocholic acid isomer 3
## HU_011 3.928441 3.536033 3.467331
## HU_014 4.286770 4.157624 4.170019
## HU_015 4.273123 4.298947 4.045842
## HU_017 4.606753 2.519658 2.687939
## HU_018 4.641004 4.743202 4.763984
## HU_019 4.429628 3.395705 3.371074
## Heptylmalonic acid Hexanoylglycine Hippuric acid
## HU_011 4.299342 3.700495 4.281181
## HU_014 4.587917 4.288872 4.274765
## HU_015 4.245115 4.154405 4.030601
## HU_017 4.101909 4.076289 4.437759
## HU_018 4.270874 4.575928 4.105510
## HU_019 4.417992 3.904992 4.297234
## Hydroxybenzyl alcohol isomer Hydroxyphenyllactic acid
## HU_011 4.238096 3.959217
## HU_014 3.602194 4.774698
## HU_015 3.948782 3.457264
## HU_017 3.368220 3.805230
## HU_018 4.324214 4.567749
## HU_019 4.043065 4.413443
## Hydroxysuberic acid isomer 1 Hydroxysuberic acid isomer 2
## HU_011 4.144705 4.295285
## HU_014 3.914818 4.351692
## HU_015 4.118942 4.050348
## HU_017 4.016532 4.476785
## HU_018 4.513977 4.474938
## HU_019 4.522243 4.145574
## Isovalerylalanine isomer Ketoleucine Kynurenic acid Malic acid
## HU_011 3.878689 3.522784 4.012747 3.534347
## HU_014 4.167564 3.861882 4.068847 4.069774
## HU_015 4.427536 3.839057 4.157414 3.696515
## HU_017 4.377871 4.034678 4.392389 3.940602
## HU_018 4.700258 4.078886 4.296854 4.231243
## HU_019 4.067620 4.030812 4.323642 4.333562
## Methoxysalicylic acid isomer
## HU_011 4.060952
## HU_014 4.112547
## HU_015 4.288847
## HU_017 4.458437
## HU_018 4.189123
## HU_019 4.562835
## Methyl (hydroxymethyl)pyrrolidine-carboxylate/Methyl (hydroxy)piperidine-carboxylate
## HU_011 3.899313
## HU_014 4.233935
## HU_015 4.520556
## HU_017 4.355592
## HU_018 4.407202
## HU_019 4.232537
## Methylinosine Mevalonic acid isomer 1 Monoethyl phthalate
## HU_011 3.979667 3.329769 4.186150
## HU_014 4.191845 4.018856 3.347641
## HU_015 4.362143 1.551281 3.824039
## HU_017 4.272384 2.800934 3.091728
## HU_018 4.487805 4.112110 3.655938
## HU_019 4.378914 4.144182 4.240828
## N-Acetyl-aspartic acid N-Acetylisoleucine N-Acetylleucine
## HU_011 4.117673 4.093393 3.411936
## HU_014 4.428008 4.306259 4.478246
## HU_015 4.205715 4.268660 4.266854
## HU_017 4.385727 4.017203 4.027337
## HU_018 4.253549 4.114619 3.237244
## HU_019 4.363792 4.483260 4.370739
## N-Acetyltryptophan N-Acetyltryptophan isomer 3
## HU_011 3.792115 4.559495
## HU_014 4.484242 4.038887
## HU_015 4.254061 4.333962
## HU_017 3.645018 4.621739
## HU_018 4.193701 3.276002
## HU_019 4.221705 4.174604
## N2-Acetylaminoadipic acid N4-Acetylcytidine Nicotinuric acid isomer
## HU_011 3.631931 4.361610 3.848278
## HU_014 4.493698 4.518477 4.441710
## HU_015 3.904043 3.885826 4.240330
## HU_017 3.997636 4.496160 4.343148
## HU_018 4.330822 4.685971 4.044958
## HU_019 4.210520 4.468025 4.452897
## Ortho-Hydroxyphenylacetic acid Oxoglutaric acid p-Anisic acid
## HU_011 3.870825 2.997953 3.841620
## HU_014 4.658541 3.993253 4.678148
## HU_015 4.001141 3.482831 3.455275
## HU_017 4.296011 3.947712 2.890224
## HU_018 4.679458 3.955677 3.247603
## HU_019 4.295495 4.195985 3.952277
## p-Hydroxyhippuric acid p-Hydroxymandelic acid
## HU_011 4.198435 4.140949
## HU_014 4.621760 3.818508
## HU_015 3.835598 4.221860
## HU_017 4.166668 4.421014
## HU_018 4.592458 4.703186
## HU_019 4.114812 4.096616
## p-Hydroxyphenylacetic acid Pantothenic acid Pentose
## HU_011 4.057362 4.367247 4.119872
## HU_014 3.867961 4.483832 4.219938
## HU_015 4.198771 4.281965 4.354551
## HU_017 4.138231 4.201390 4.294260
## HU_018 4.348636 4.367093 4.465690
## HU_019 4.181577 4.121433 4.250880
## Phe-Tyr-Asp (and isomers) Porphobilinogen Pyridoxic acid isomer 1
## HU_011 4.379156 3.873927 4.264819
## HU_014 4.227932 4.181048 4.103788
## HU_015 4.004176 4.136767 3.887147
## HU_017 4.214129 4.162675 3.856186
## HU_018 4.154741 4.461157 4.602857
## HU_019 4.340768 4.170573 4.069686
## Pyridylacetylglycine Pyrocatechol sulfate Pyroglutamic acid
## HU_011 4.042992 4.452942 4.013843
## HU_014 4.210327 4.281094 4.188313
## HU_015 4.099646 4.239741 4.202476
## HU_017 4.309022 4.186333 4.209444
## HU_018 4.386013 4.060466 4.246487
## HU_019 4.398879 4.282089 4.184347
## Pyrroledicarboxylic acid Pyruvic acid Quinic acid Salicylic acid
## HU_011 3.854579 3.229445 4.128023 3.925518
## HU_014 4.059364 3.843606 4.168761 4.035196
## HU_015 4.426634 3.555714 4.295171 4.588327
## HU_017 3.763358 3.766176 4.533188 3.847885
## HU_018 3.828249 3.985018 3.685546 3.695891
## HU_019 4.317047 3.911799 4.459420 4.100363
## Sebacic acid Suberic acid Sulfosalicylic acid isomer Taurine
## HU_011 4.298555 4.283358 4.724543 4.294956
## HU_014 4.316859 4.521646 3.968791 5.143374
## HU_015 4.387094 4.159625 3.946592 4.525365
## HU_017 4.026013 4.125570 3.560990 4.821052
## HU_018 4.516985 4.452634 4.320034 4.544508
## HU_019 4.547073 4.535423 4.480640 3.999298
## Testosterone glucuronide Tetrahydrohippuric acid
## HU_011 4.292437 3.409692
## HU_014 3.467556 4.766827
## HU_015 4.325043 3.407598
## HU_017 4.306862 4.522244
## HU_018 4.589208 4.296404
## HU_019 4.010066 3.764092
## Threo-3-Phenylserine Threonic acid/Erythronic acid Tryptophan
## HU_011 4.274910 4.313963 4.006518
## HU_014 4.153934 4.473729 4.421590
## HU_015 3.457296 4.124348 4.438306
## HU_017 3.927525 4.558518 4.542105
## HU_018 4.246966 4.446222 4.217120
## HU_019 4.269736 4.367592 4.558531
## Valerylglycine isomer 1 Valerylglycine isomer 2 Xanthosine
## HU_011 4.016261 3.889079 4.075880
## HU_014 3.881005 4.181766 4.195762
## HU_015 4.187176 4.254695 4.124493
## HU_017 4.147544 4.290660 4.250258
## HU_018 4.104498 4.138196 4.361709
## HU_019 4.065452 4.300930 4.199196sampleMetadata## age bmi gender
## HU_011 29.0 19.75 M
## HU_014 59.0 22.64 F
## HU_015 42.0 22.72 M
## HU_017 41.0 23.03 M
## HU_018 34.0 20.96 M
## HU_019 35.0 23.41 M
## HU_020 59.0 17.10 M
## HU_021 34.0 23.36 M
## HU_022 51.0 28.23 F
## HU_023 51.0 29.55 M
## HU_024 57.0 29.86 M
## HU_025 53.0 21.60 M
## HU_026 34.0 23.46 F
## HU_027 37.0 24.82 M
## HU_028 41.0 23.92 F
## HU_029 37.0 27.78 M
## HU_030 49.0 25.88 M
## HU_031 25.0 20.76 M
## HU_032 38.0 24.09 F
## HU_033 44.0 18.36 F
## HU_034 52.0 23.37 M
## HU_035 37.0 20.70 F
## HU_036 47.0 29.51 M
## HU_037 35.0 25.62 M
## HU_038 52.0 22.72 M
## HU_039 45.0 24.90 M
## HU_040 24.0 26.54 M
## HU_041 28.0 23.67 M
## HU_042 36.0 19.75 M
## HU_043 42.0 29.04 M
## HU_044 57.0 25.46 F
## HU_045 46.0 20.81 F
## HU_046 35.0 24.84 M
## HU_047 43.0 25.00 F
## HU_048 39.0 19.49 F
## HU_049 50.0 27.85 M
## HU_050 30.0 24.21 M
## HU_051 24.0 23.23 F
## HU_052 51.0 20.06 F
## HU_053 49.0 25.88 M
## HU_054 29.0 20.76 M
## HU_055 58.0 24.89 F
## HU_056 41.0 21.15 M
## HU_057 57.0 27.16 M
## HU_058 45.0 26.70 M
## HU_060 55.0 28.72 F
## HU_061 44.0 25.35 F
## HU_062 34.0 22.22 M
## HU_063 35.0 21.01 F
## HU_064 32.0 21.94 F
## HU_065 54.0 21.87 M
## HU_066 25.0 22.53 F
## HU_067 40.0 19.31 F
## HU_068 37.0 27.22 F
## HU_069 39.0 24.38 M
## HU_070 58.0 18.71 M
## HU_072 47.0 27.13 M
## HU_073 35.0 25.38 M
## HU_074 42.0 20.94 F
## HU_075 38.0 21.05 M
## HU_076 47.0 26.70 M
## HU_077 27.0 21.15 M
## HU_078 46.0 25.18 M
## HU_079 47.0 23.55 M
## HU_080 21.0 19.72 F
## HU_081 25.0 17.84 F
## HU_082 49.0 23.15 M
## HU_083 50.0 29.76 M
## HU_084 62.0 23.80 F
## HU_085 23.0 22.86 M
## HU_086 33.0 23.51 M
## HU_087 38.0 23.80 F
## HU_088 50.0 21.78 F
## HU_089 31.0 23.70 M
## HU_090 46.0 19.79 M
## HU_091 61.0 26.12 M
## HU_092 40.0 21.83 M
## HU_093 53.0 21.71 M
## HU_094 32.0 23.29 M
## HU_095 27.0 27.33 M
## HU_097 50.0 26.78 M
## HU_098 46.0 20.45 M
## HU_099 23.0 21.30 M
## HU_100 47.0 21.22 F
## HU_101 39.0 23.70 M
## HU_102 59.0 24.03 F
## HU_103 49.0 26.79 M
## HU_105 47.0 22.96 M
## HU_106 42.0 27.34 M
## HU_107 46.0 24.22 M
## HU_108 25.0 23.81 M
## HU_109 32.0 22.68 M
## HU_110 50.0 20.90 F
## HU_112 55.0 25.36 M
## HU_113 44.0 23.05 M
## HU_114 58.0 29.38 M
## HU_115 46.0 27.24 F
## HU_116 28.0 20.96 F
## HU_117 24.0 22.86 M
## HU_118 30.0 21.64 F
## HU_119 50.0 24.44 F
## HU_120 32.0 23.88 F
## HU_121 26.0 20.57 M
## HU_122 48.0 23.03 M
## HU_123 49.0 24.39 M
## HU_124 34.0 22.22 M
## HU_125 58.0 25.47 M
## HU_126 45.0 24.70 M
## HU_127 45.0 25.62 M
## HU_129 47.0 29.32 M
## HU_130 33.0 26.06 M
## HU_131 42.0 23.12 M
## HU_132 38.0 26.67 F
## HU_133 53.0 25.43 M
## HU_134 48.0 22.89 M
## HU_135 31.0 24.93 M
## HU_136 52.0 20.81 F
## HU_137 28.0 22.22 M
## HU_138 42.0 21.88 M
## HU_139 47.0 23.03 M
## HU_140 49.0 26.59 M
## HU_142 25.0 20.98 M
## HU_143 52.0 23.15 F
## HU_144 38.0 29.54 M
## HU_145 27.0 29.09 M
## HU_146 42.0 24.21 M
## HU_147 60.0 31.74 M
## HU_148 55.0 30.48 F
## HU_149 35.0 19.49 F
## HU_150 49.0 27.24 F
## HU_152 26.0 17.58 F
## HU_154 35.0 27.71 F
## HU_155 48.0 20.45 F
## HU_156 36.0 16.85 F
## HU_157 43.0 21.95 F
## HU_158 50.0 25.48 F
## HU_159 37.0 21.72 F
## HU_160 31.0 24.17 F
## HU_162 50.0 29.03 F
## HU_163 49.0 23.15 F
## HU_164 45.0 25.63 F
## HU_166 40.0 19.72 F
## HU_167 55.0 20.57 F
## HU_168 37.0 20.76 F
## HU_169 53.0 19.14 F
## HU_170 50.0 24.61 F
## HU_171 29.0 21.37 F
## HU_172 55.0 21.36 F
## HU_173 55.0 20.28 F
## HU_174 42.0 31.64 F
## HU_175 35.0 21.26 F
## HU_177 59.0 28.58 F
## HU_179 33.0 26.57 F
## HU_180 53.0 23.74 F
## HU_181 49.0 22.46 F
## HU_182 43.0 23.74 F
## HU_183 46.0 19.13 F
## HU_184 37.0 25.33 F
## HU_185 42.0 21.09 F
## HU_186 44.0 22.10 F
## HU_187 21.0 19.95 F
## HU_188 22.0 24.22 F
## HU_189 39.0 19.43 F
## HU_190 28.0 25.93 M
## HU_191 36.0 26.12 M
## HU_192 31.0 24.22 M
## HU_193 35.0 21.78 F
## HU_194 40.0 28.04 F
## HU_195 26.0 18.42 F
## HU_196 27.0 21.10 F
## HU_197 26.0 20.72 M
## HU_198 35.0 22.98 M
## HU_199 33.0 21.04 M
## HU_200 46.0 23.89 M
## HU_201 34.0 20.24 M
## HU_202 42.0 28.06 M
## HU_203 25.0 19.95 F
## HU_204 31.0 29.06 M
## HU_205 33.0 28.37 M
## HU_206 45.0 22.15 F
## HU_207 33.0 19.47 F
## HU_208 27.0 18.61 F
## HU_209 17.5 21.48 Fsummary(sampleMetadata)## age bmi gender
## Min. :17.5 Min. :16.85 M:100
## 1st Qu.:33.0 1st Qu.:21.12 F: 83
## Median :42.0 Median :23.36
## Mean :40.9 Mean :23.61
## 3rd Qu.:49.0 3rd Qu.:25.62
## Max. :62.0 Max. :31.7423.2 Principal Component Analysis (PCA)
We perform a PCA on the dataMatrix matrix (samples as rows, variables as columns), with the opls method:
sacurine.pca <- opls(dataMatrix)## PCA
## 183 samples x 109 variables
## standard scaling of predictors
## R2X(cum) pre ort
## Total 0.501 8 0genderFc <- sampleMetadata[, "gender"]
plot(sacurine.pca, typeVc = "x-score",
parAsColFcVn = genderFc, parEllipsesL = TRUE)23.3 Partial least-squares: PLS and PLS-DA
For PLS (and OPLS), the Y response(s) must be provided to the opls method. Y can be either a numeric vector (respectively matrix) for single (respectively multiple) (O)PLS regression, or a character factor for (O)PLS-DA classification as in the following example with the gender qualitative response:
sacurine.plsda <- opls(dataMatrix, genderFc)## PLS-DA
## 183 samples x 109 variables and 1 response
## standard scaling of predictors and response(s)
## R2X(cum) R2Y(cum) Q2(cum) RMSEE pre ort pR2Y pQ2
## Total 0.275 0.73 0.584 0.262 3 0 0.05 0.05genderFc## [1] M F M M M M M M F M M M F M F M M M F F M F M M M M M M M M F F M F F
## [36] M M F F M M F M M M F F M F F M F F F M M M M F M M M M M F F M M F M
## [71] M F F M M M M M M M M M M F M F M M M M M M F M M M F F M F F F M M M
## [106] M M M M M M M F M M M F M M M M M F M M M M F F F F F F F F F F F F F
## [141] F F F F F F F F F F F F F F F F F F F F F F F M M M F F F F M M M M M
## [176] M F M M F F F F
## Levels: M Fhead(dataMatrix)## (2-methoxyethoxy)propanoic acid isomer (gamma)Glu-Leu/Ile
## HU_011 3.019766 3.888479
## HU_014 3.814339 4.277149
## HU_015 3.519691 4.195649
## HU_017 2.562183 4.323760
## HU_018 3.781922 4.629329
## HU_019 4.161074 4.412266
## 1-Methyluric acid 1-Methylxanthine 1,3-Dimethyluric acid
## HU_011 3.869006 3.717259 3.535461
## HU_014 3.837704 3.776851 3.932581
## HU_015 4.102254 4.291665 3.955376
## HU_017 4.538520 4.432216 4.228491
## HU_018 4.178829 4.117360 4.005545
## HU_019 4.516805 4.562052 4.320582
## 1,7-Dimethyluric acid 2-acetamido-4-methylphenyl acetate
## HU_011 3.325199 4.204754
## HU_014 4.025125 5.181858
## HU_015 3.972904 3.885680
## HU_017 4.109927 4.237915
## HU_018 4.024092 1.852994
## HU_019 4.326856 4.080681
## 2-Aminoadipic acid 2-Hydroxybenzyl alcohol 2-Isopropylmalic acid
## HU_011 4.080204 4.560049 3.466916
## HU_014 4.359246 3.158212 3.942746
## HU_015 4.249111 4.290525 3.539600
## HU_017 4.231404 3.644976 3.152084
## HU_018 4.323679 4.095923 4.490116
## HU_019 4.244485 4.428005 4.156567
## 2-Methylhippuric acid 2,2-Dimethylglutaric acid
## HU_011 4.297716 3.799720
## HU_014 3.833793 4.192342
## HU_015 4.199262 4.146924
## HU_017 3.865260 4.233270
## HU_018 4.271223 4.755177
## HU_019 3.831930 4.333599
## 3-Hydroxybenzyl alcohol 3-Hydroxyphenylacetic acid
## HU_011 3.502958 4.672721
## HU_014 4.370053 4.490127
## HU_015 3.990814 4.416155
## HU_017 4.151260 3.960912
## HU_018 4.373425 4.247532
## HU_019 1.446237 4.164327
## 3-Indole carboxylic acid glucuronide 3-Methyl-2-oxovaleric acid
## HU_011 3.548979 3.956110
## HU_014 4.344955 4.062870
## HU_015 4.174503 4.420565
## HU_017 4.688053 4.146152
## HU_018 3.276676 4.351114
## HU_019 4.206905 4.341494
## 3-Methylcrotonylglycine 3,3-Dimethylglutaric acid
## HU_011 4.204465 4.223994
## HU_014 4.055144 4.486961
## HU_015 4.148095 4.137063
## HU_017 4.193130 4.200239
## HU_018 4.225720 4.569052
## HU_019 4.127074 4.195226
## 3,4-Dihydroxybenzeneacetic acid
## HU_011 3.400454
## HU_014 4.366695
## HU_015 3.965742
## HU_017 4.121298
## HU_018 4.373747
## HU_019 2.320550
## 3,5-dihydroxybenzoic acid/3,4-dihydroxybenzoic acid
## HU_011 4.494138
## HU_014 4.118021
## HU_015 4.284274
## HU_017 4.118248
## HU_018 4.077463
## HU_019 4.107163
## 3,7-Dimethyluric acid 4-Acetamidobutanoic acid isomer 2
## HU_011 4.233820 4.046984
## HU_014 3.596651 4.218431
## HU_015 3.954022 3.995719
## HU_017 3.995039 4.006450
## HU_018 3.908515 4.564357
## HU_019 4.720603 4.193068
## 4-Acetamidobutanoic acid isomer 3 4-Hydroxybenzoic acid
## HU_011 3.964380 4.581811
## HU_014 4.087865 4.675483
## HU_015 4.031485 4.248248
## HU_017 3.884681 4.171788
## HU_018 4.347509 4.660293
## HU_019 4.040541 4.335561
## 4-Methylhippuric acid/3-Methylhippuric acid
## HU_011 3.242186
## HU_014 3.838007
## HU_015 4.723900
## HU_017 3.617350
## HU_018 4.285848
## HU_019 3.430342
## 5-Hydroxyindoleacetic acid 5-Sulfosalicylic acid
## HU_011 4.307545 4.023477
## HU_014 4.402027 4.083692
## HU_015 3.975413 4.232119
## HU_017 4.168655 3.088972
## HU_018 4.502182 4.142686
## HU_019 4.281092 3.950241
## 6-(2-hydroxyethoxy)-6-oxohexanoic acid
## HU_011 3.758640
## HU_014 4.329163
## HU_015 3.994170
## HU_017 4.436174
## HU_018 4.442814
## HU_019 4.260599
## 6-(carboxymethoxy)-hexanoic acid 9-Methylxanthine
## HU_011 3.445392 4.403909
## HU_014 3.999589 4.211293
## HU_015 4.039267 4.073960
## HU_017 4.084428 4.257367
## HU_018 4.527800 3.662754
## HU_019 4.114818 4.262501
## Acetaminophen glucuronide Acetylphenylalanine
## HU_011 1.64620136 4.169514
## HU_014 0.09467123 4.515993
## HU_015 -0.15947672 4.083460
## HU_017 0.32143853 3.767910
## HU_018 1.76127463 4.187942
## HU_019 4.62568088 4.292496
## alpha-N-Phenylacetyl-glutamine Aminosalicyluric acid
## HU_011 4.406638 4.125306
## HU_014 4.362682 3.942512
## HU_015 4.101540 4.004895
## HU_017 4.173137 4.277246
## HU_018 4.332330 4.307816
## HU_019 4.366653 3.908610
## Asp-Leu/Ile isomer 1 Asp-Leu/Ile isomer 2 Aspartic acid
## HU_011 3.565669 3.706871 4.262679
## HU_014 3.852859 3.624547 4.278906
## HU_015 3.879881 3.965623 4.225658
## HU_017 3.564683 4.000451 4.476138
## HU_018 4.710114 4.414012 4.460986
## HU_019 4.551170 4.417869 4.545151
## Azelaic acid Benzoic acid isomer Chenodeoxycholic acid isomer
## HU_011 4.419660 3.867245 3.507941
## HU_014 4.331720 4.830236 3.925771
## HU_015 4.105070 3.371990 4.765679
## HU_017 4.017999 3.724525 4.058410
## HU_018 4.320763 4.593359 4.379709
## HU_019 4.641622 4.475130 4.120224
## Cinnamoylglycine Citric acid Dehydroepiandrosterone 3-glucuronide
## HU_011 3.981493 4.077505 4.276799
## HU_014 3.381453 4.418117 3.781079
## HU_015 3.773393 4.179830 4.039523
## HU_017 4.213982 4.218916 3.960037
## HU_018 2.636678 4.294479 4.178258
## HU_019 4.071694 4.386380 4.018968
## Dehydroepiandrosterone sulfate Deoxyhexose Dimethylguanosine
## HU_011 4.462774 3.760569 4.052598
## HU_014 3.806104 3.809186 4.269907
## HU_015 3.193502 4.226145 4.197532
## HU_017 4.165680 3.997357 4.350023
## HU_018 4.363253 4.084736 4.408429
## HU_019 3.986997 4.296965 4.310144
## FMNH2 Fumaric acid Gentisic acid Glu-Val
## HU_011 3.565083 3.567561 4.300974 3.706666
## HU_014 4.208395 3.840097 4.584677 4.310927
## HU_015 4.034409 4.384064 4.764176 4.289509
## HU_017 4.233037 3.416630 4.062663 4.376818
## HU_018 4.597364 4.091964 4.431808 4.721889
## HU_019 4.199745 4.012107 4.238883 4.392128
## Gluconic acid and/or isomers Glucuronic acid and/or isomers
## HU_011 4.288424 4.271366
## HU_014 4.586464 4.701159
## HU_015 4.096407 4.123025
## HU_017 4.743170 4.593438
## HU_018 4.614798 4.461186
## HU_019 4.334139 4.461209
## Glyceric acid Glycocholic acid isomer 2 Glycocholic acid isomer 3
## HU_011 3.928441 3.536033 3.467331
## HU_014 4.286770 4.157624 4.170019
## HU_015 4.273123 4.298947 4.045842
## HU_017 4.606753 2.519658 2.687939
## HU_018 4.641004 4.743202 4.763984
## HU_019 4.429628 3.395705 3.371074
## Heptylmalonic acid Hexanoylglycine Hippuric acid
## HU_011 4.299342 3.700495 4.281181
## HU_014 4.587917 4.288872 4.274765
## HU_015 4.245115 4.154405 4.030601
## HU_017 4.101909 4.076289 4.437759
## HU_018 4.270874 4.575928 4.105510
## HU_019 4.417992 3.904992 4.297234
## Hydroxybenzyl alcohol isomer Hydroxyphenyllactic acid
## HU_011 4.238096 3.959217
## HU_014 3.602194 4.774698
## HU_015 3.948782 3.457264
## HU_017 3.368220 3.805230
## HU_018 4.324214 4.567749
## HU_019 4.043065 4.413443
## Hydroxysuberic acid isomer 1 Hydroxysuberic acid isomer 2
## HU_011 4.144705 4.295285
## HU_014 3.914818 4.351692
## HU_015 4.118942 4.050348
## HU_017 4.016532 4.476785
## HU_018 4.513977 4.474938
## HU_019 4.522243 4.145574
## Isovalerylalanine isomer Ketoleucine Kynurenic acid Malic acid
## HU_011 3.878689 3.522784 4.012747 3.534347
## HU_014 4.167564 3.861882 4.068847 4.069774
## HU_015 4.427536 3.839057 4.157414 3.696515
## HU_017 4.377871 4.034678 4.392389 3.940602
## HU_018 4.700258 4.078886 4.296854 4.231243
## HU_019 4.067620 4.030812 4.323642 4.333562
## Methoxysalicylic acid isomer
## HU_011 4.060952
## HU_014 4.112547
## HU_015 4.288847
## HU_017 4.458437
## HU_018 4.189123
## HU_019 4.562835
## Methyl (hydroxymethyl)pyrrolidine-carboxylate/Methyl (hydroxy)piperidine-carboxylate
## HU_011 3.899313
## HU_014 4.233935
## HU_015 4.520556
## HU_017 4.355592
## HU_018 4.407202
## HU_019 4.232537
## Methylinosine Mevalonic acid isomer 1 Monoethyl phthalate
## HU_011 3.979667 3.329769 4.186150
## HU_014 4.191845 4.018856 3.347641
## HU_015 4.362143 1.551281 3.824039
## HU_017 4.272384 2.800934 3.091728
## HU_018 4.487805 4.112110 3.655938
## HU_019 4.378914 4.144182 4.240828
## N-Acetyl-aspartic acid N-Acetylisoleucine N-Acetylleucine
## HU_011 4.117673 4.093393 3.411936
## HU_014 4.428008 4.306259 4.478246
## HU_015 4.205715 4.268660 4.266854
## HU_017 4.385727 4.017203 4.027337
## HU_018 4.253549 4.114619 3.237244
## HU_019 4.363792 4.483260 4.370739
## N-Acetyltryptophan N-Acetyltryptophan isomer 3
## HU_011 3.792115 4.559495
## HU_014 4.484242 4.038887
## HU_015 4.254061 4.333962
## HU_017 3.645018 4.621739
## HU_018 4.193701 3.276002
## HU_019 4.221705 4.174604
## N2-Acetylaminoadipic acid N4-Acetylcytidine Nicotinuric acid isomer
## HU_011 3.631931 4.361610 3.848278
## HU_014 4.493698 4.518477 4.441710
## HU_015 3.904043 3.885826 4.240330
## HU_017 3.997636 4.496160 4.343148
## HU_018 4.330822 4.685971 4.044958
## HU_019 4.210520 4.468025 4.452897
## Ortho-Hydroxyphenylacetic acid Oxoglutaric acid p-Anisic acid
## HU_011 3.870825 2.997953 3.841620
## HU_014 4.658541 3.993253 4.678148
## HU_015 4.001141 3.482831 3.455275
## HU_017 4.296011 3.947712 2.890224
## HU_018 4.679458 3.955677 3.247603
## HU_019 4.295495 4.195985 3.952277
## p-Hydroxyhippuric acid p-Hydroxymandelic acid
## HU_011 4.198435 4.140949
## HU_014 4.621760 3.818508
## HU_015 3.835598 4.221860
## HU_017 4.166668 4.421014
## HU_018 4.592458 4.703186
## HU_019 4.114812 4.096616
## p-Hydroxyphenylacetic acid Pantothenic acid Pentose
## HU_011 4.057362 4.367247 4.119872
## HU_014 3.867961 4.483832 4.219938
## HU_015 4.198771 4.281965 4.354551
## HU_017 4.138231 4.201390 4.294260
## HU_018 4.348636 4.367093 4.465690
## HU_019 4.181577 4.121433 4.250880
## Phe-Tyr-Asp (and isomers) Porphobilinogen Pyridoxic acid isomer 1
## HU_011 4.379156 3.873927 4.264819
## HU_014 4.227932 4.181048 4.103788
## HU_015 4.004176 4.136767 3.887147
## HU_017 4.214129 4.162675 3.856186
## HU_018 4.154741 4.461157 4.602857
## HU_019 4.340768 4.170573 4.069686
## Pyridylacetylglycine Pyrocatechol sulfate Pyroglutamic acid
## HU_011 4.042992 4.452942 4.013843
## HU_014 4.210327 4.281094 4.188313
## HU_015 4.099646 4.239741 4.202476
## HU_017 4.309022 4.186333 4.209444
## HU_018 4.386013 4.060466 4.246487
## HU_019 4.398879 4.282089 4.184347
## Pyrroledicarboxylic acid Pyruvic acid Quinic acid Salicylic acid
## HU_011 3.854579 3.229445 4.128023 3.925518
## HU_014 4.059364 3.843606 4.168761 4.035196
## HU_015 4.426634 3.555714 4.295171 4.588327
## HU_017 3.763358 3.766176 4.533188 3.847885
## HU_018 3.828249 3.985018 3.685546 3.695891
## HU_019 4.317047 3.911799 4.459420 4.100363
## Sebacic acid Suberic acid Sulfosalicylic acid isomer Taurine
## HU_011 4.298555 4.283358 4.724543 4.294956
## HU_014 4.316859 4.521646 3.968791 5.143374
## HU_015 4.387094 4.159625 3.946592 4.525365
## HU_017 4.026013 4.125570 3.560990 4.821052
## HU_018 4.516985 4.452634 4.320034 4.544508
## HU_019 4.547073 4.535423 4.480640 3.999298
## Testosterone glucuronide Tetrahydrohippuric acid
## HU_011 4.292437 3.409692
## HU_014 3.467556 4.766827
## HU_015 4.325043 3.407598
## HU_017 4.306862 4.522244
## HU_018 4.589208 4.296404
## HU_019 4.010066 3.764092
## Threo-3-Phenylserine Threonic acid/Erythronic acid Tryptophan
## HU_011 4.274910 4.313963 4.006518
## HU_014 4.153934 4.473729 4.421590
## HU_015 3.457296 4.124348 4.438306
## HU_017 3.927525 4.558518 4.542105
## HU_018 4.246966 4.446222 4.217120
## HU_019 4.269736 4.367592 4.558531
## Valerylglycine isomer 1 Valerylglycine isomer 2 Xanthosine
## HU_011 4.016261 3.889079 4.075880
## HU_014 3.881005 4.181766 4.195762
## HU_015 4.187176 4.254695 4.124493
## HU_017 4.147544 4.290660 4.250258
## HU_018 4.104498 4.138196 4.361709
## HU_019 4.065452 4.300930 4.199196