Real Datasets Application

 

Description

Gene expression data from Khan et al. (2001). This data set contains 83 samples with 2308 genes: 29 cases of Ewing sarcoma (EWS), coded 1, 11 cases of Burkitt lymphoma (BL), coded 2, 18 cases of neuroblastoma (NB), coded 3, 25 cases of rhabdomyosarcoma (RMS), coded 4. A total of 63 training samples and 25 test samples are provided in Khan et al. (2001). Five of the test set are non-SRBCT and are not considered here. The training sample indexes correspond to 1:65 and the test sample indexes (without non-SRBCT sample) correspond to 66:83.

Standard PCA method

library(plsgenomics)
# For any news related to the 'plsgenomics' package (update, corrected bugs), please check http://thoth.inrialpes.fr/people/gdurif/
# C++ based sparse PLS routines will soon be available on the CRAN in the new 'fastPLS' package.
library(MultiGroupO)
data(SRBCT)
 mydata<-SRBCT$X
 mydata<-mydata[,1:5]
 groups<-as.factor(SRBCT$Y)
 pca(datos=mydata,grupos=groups,Plot=TRUE,center=TRUE,scale=FALSE)

# $loadings
#              PC1         PC2        PC3          PC4          PC5
# [1,] -0.94728054  0.24001708  0.1989556  0.073801089 -0.004632259
# [2,] -0.13989846 -0.16047800 -0.1118758 -0.970072631  0.033438370
# [3,]  0.18054603  0.94484241 -0.2223145 -0.157444629 -0.021526400
# [4,]  0.22108232  0.14600740  0.9356202 -0.169465632 -0.160314251
# [5,] -0.04017129 -0.05092408 -0.1519591 -0.002253519 -0.986253706
# 
# $variates
#               PC1           PC2         PC3          PC4           PC5
#  [1,] -1.67856734  0.4079880063 -0.02241524  0.411531062 -0.1533598693
#  [2,] -0.21804365  0.0353967641 -0.35318728  0.308196478  0.1512264910
#  [3,] -1.78092361  0.2809271853  0.03216541  0.399140376  0.0642475642
#  [4,]  0.27707958 -0.7137731389 -0.32594713  0.231513374  0.0705114323
#  [5,] -1.33172703 -0.3566092997  0.11843153  0.302386587 -0.0247454847
#  [6,] -0.61819806  0.0008864521 -0.20045600  0.335464257 -0.0485580316
#  [7,] -0.38616443  0.0490137475 -0.17974845  0.249450807 -0.0437162704
#  [8,] -1.30203326 -0.2271466393  0.11129535  0.331562426 -0.1373604682
#  [9,] -0.91223009 -0.0529229324 -0.05866381  0.372645295 -0.0766223702
# [10,] -0.57431782 -0.3629691448 -0.15696626  0.211832185  0.0226571473
# [11,] -2.12322787  0.0893237052  0.31135457  0.452348803 -0.1207324174
# [12,] -0.76242684 -0.3497289670 -0.01743087  0.376028044 -0.1178658699
# [13,] -0.84654213 -0.2042954368  0.25730831  0.265738571 -0.1591611445
# [14,]  0.70174005  0.6553666039  0.50602520 -0.164504642 -0.0928488055
# [15,]  0.40851695 -0.4117042562 -0.48359776  0.175410060 -0.0400886269
# [16,]  0.54404432  0.2856977809 -0.64829398  0.160581028 -0.1816327039
# [17,] -0.97382499  1.0539560060 -0.26513531  0.207302097 -0.1119526626
# [18,]  0.82911920  1.2994826330  0.41744126 -0.256760018 -0.0276008605
# [19,]  0.73416847  0.9854924318  0.41669253 -0.178448913 -0.0033259140
# [20,]  0.19487659  0.3346419706  0.97759377  0.055351019 -0.0044948652
# [21,] -0.78274193 -0.2472377511 -0.15989915  0.394356833  0.0659659897
# [22,]  1.10341154 -0.4984696627  0.24168347  0.109430767  0.0773652018
# [23,]  0.62603357  0.7670014643  0.20805516 -0.076614433  0.0611049959
# [24,]  1.34908148 -0.0592679453  0.52510894 -0.027738560 -0.1680024700
# [25,]  1.58928423  0.5468119419  0.43307200 -0.191718417  0.0083639769
# [26,]  1.37023042 -0.9229849418  0.65211945  0.087878189  0.0179268446
# [27,]  1.31365525 -0.1628517205  0.55931348  0.035651783  0.1083538911
# [28,]  1.22870879 -0.2934555708 -0.62478614  0.193831743 -0.0402473372
# [29,]  1.18609440  0.5382514049 -0.75427979  0.079185705 -0.0041571822
# [30,]  1.10351734  0.0918803747 -0.47484516  0.119216014 -0.1474312384
# [31,]  1.19310090 -0.7899329660 -0.58285432  0.202442671 -0.2678543431
# [32,]  0.22208054  0.3163119242 -0.53607758  0.053229115 -0.0863587151
# [33,]  0.50232425  1.6699724029 -0.83194464 -0.080521760 -0.1733855942
# [34,]  0.63572183 -0.0607644021 -0.48678507  0.139324759  0.0478879819
# [35,]  0.94231336 -0.3372141669  1.02785346  0.026911819 -0.0020463708
# [36,]  0.19019432  0.7567766580  1.15874139 -0.203999642 -0.1221636734
# [37,]  0.79037962  2.2083711869  0.51497309 -0.360622421 -0.0307591633
# [38,]  0.98541194  0.2631986609  0.19384815  0.025621240  0.1183392538
# [39,]  0.92240203 -0.7282071267  0.73168477  0.084156401  0.0447847177
# [40,]  0.46236121  0.3082099166  0.51585105  0.001310997  0.0642385594
# [41,]  0.50172024  0.3975934233  0.83054886  0.018956414  0.0604932540
# [42,]  0.88928386  0.8206476271  0.54902440 -0.149987730 -0.0194574400
# [43,]  1.09651840 -0.3313917207  0.97289301 -0.108293043 -0.0648443022
# [44,] -1.24036595  0.2710232627  0.18750880  0.354547150  0.1675517223
# [45,] -0.80086562 -0.7151095320  0.01273562  0.183658951 -0.0057240936
# [46,]  0.21174542 -0.6804132915  1.19509963 -0.040118566 -0.0437583165
# [47,]  0.29117431 -0.1385115736  0.94825797  0.011499409  0.0260075991
# [48,]  0.26736439 -0.7042684593  0.90433002 -0.065814504 -0.0349132308
# [49,]  0.78928953 -0.0217484490  0.67243515 -0.247472893  0.0003969374
# [50,]  0.08330340 -0.4896842028  0.74724280  0.126095527  0.0451927414
# [51,]  0.20931203 -0.7421378374 -0.54055378 -0.500345784 -0.3660624017
# [52,]  0.07010603 -0.1755805707  0.74997378  0.178103683  0.1474002320
# [53,] -1.11053994 -0.0254422667 -0.25366979 -0.555311781  0.0030640513
# [54,] -0.04110380 -1.0568532612 -0.47298085 -0.885329403 -0.1698802532
# [55,] -2.22531301 -0.3923611218  0.04470955 -0.631982133  0.0768769142
# [56,] -0.83937933 -0.4545513842 -0.31899204 -0.408983273 -0.2896033697
# [57,] -1.69352449 -0.2406806068  0.28001153  0.166224529  0.2228415260
# [58,] -0.70702173 -0.5625797851  0.04530671 -0.076927097 -0.2729976178
# [59,] -1.13818363 -0.8201899480 -0.19117424 -1.351380809  0.0281888972
# [60,] -0.49312246 -0.3020180582 -0.07971039 -0.102134354 -0.0606863154
# [61,]  0.06742049 -0.2280472555 -0.46378125 -0.089413953 -0.0199769602
# [62,] -0.08496562 -0.9279078714 -0.23412326 -0.290892162  0.2166931076
# [63,] -0.65120446  0.0329683734 -0.30548867 -0.289696720  0.1526697488
# [64,]  0.64029157 -0.0441217957 -0.52918648  0.100432448  0.1686478235
# [65,]  0.89314773 -0.9038412245 -0.48588769  0.032026401  0.2103180130
# [66,]  0.35017016  0.5488885967 -0.66597387 -0.071897066  0.0879692612
# [67,] -1.32500608  2.2697547987 -0.43703686  0.040981027  0.0616241350
# [68,] -1.04550749 -0.2088329114 -0.24831841 -0.800298362  0.1678953248
# [69,]  1.26148785 -0.0674167743 -0.72102197  0.113994450  0.0598042267
# [70,] -2.81969292  0.4263504171  0.31582445  0.433514227  0.0820331826
# [71,] -0.06075892 -0.8343390573 -0.25306175  0.009617833 -0.1421766721
# [72,] -0.56029054 -0.1200565122 -0.13227814  0.274985647 -0.0230993323
# [73,] -0.55986487 -0.3710256786 -0.15945119  0.213636976  0.0257022257
# [74,] -1.46430709  0.5760027237  0.02081738  0.281958595  0.0194752741
# [75,] -2.38489616  0.3115038758  0.04022211 -1.088046651  0.1759149570
# [76,]  1.35748512  0.5821119401 -0.78788064  0.023848691  0.1476416016
# [77,]  0.44230712 -1.0030136856 -0.37505620  0.123065228  0.0675698614
# [78,]  0.77328236  0.9834109586 -0.79219366 -0.099825686  0.0045409947
# [79,]  0.77498747  0.0544995642 -0.63579078  0.007548415  0.1279642696
# [80,]  0.87411434  0.6870883227 -0.70253381 -0.159868717  0.0624876364
# [81,]  0.57676191 -0.0261843151 -0.53007352 -0.061254961  0.0772289301
# [82,]  1.11865721 -0.9522778059 -0.50171825  0.261213105  0.2142690268
# [83,]  0.59110002 -0.5866800802 -0.44630268  0.261265247  0.0682152350
# 
# $prop_expl_var
# [1] 0.55 0.24 0.15 0.06 0.01
# 
# attr(,"class")
# [1] "pca"

Multigroup PCA method

library(plsgenomics)
data(SRBCT)
mydata<-SRBCT$X
mydata<-mydata[,1:5]
groups<-as.factor(SRBCT$Y)
mat.to.diag1<-new.cov(x=mydata,cls=groups,A=diag(ncol(mydata)))
mgpca(mat.to.diag=mat.to.diag1,mat.x=as.matrix(mydata),cls=groups,Plot=TRUE,ncomp=2,center = TRUE,scale = TRUE)

# $variates
#              [,1]         [,2]        [,3]         [,4]         [,5]
#  [1,] -1.72403001  0.508402635 -0.45492278  0.828527233  1.191417771
#  [2,] -0.20672447  0.134090675 -0.58738092  0.721960626 -0.684209083
#  [3,] -1.81731150  0.346363923 -0.23726780  0.754159429 -0.180261753
#  [4,]  0.15430112 -0.976150762 -0.57607111  0.537723073 -0.098069321
#  [5,] -1.47808450 -0.606372349 -0.11903926  0.528329253  0.398492094
#  [6,] -0.66302434  0.008941405 -0.53321498  0.748848978  0.558328904
#  [7,] -0.40779846  0.085523590 -0.43749633  0.572500626  0.460107575
#  [8,] -1.43343854 -0.422371202 -0.18924938  0.631522349  1.082242907
#  [9,] -0.97354219 -0.097064020 -0.35750545  0.805146753  0.702999438
# [10,] -0.69729481 -0.553189472 -0.43842657  0.392986080  0.156024794
# [11,] -2.21297908  0.003891979  0.05806129  0.855311928  0.907041155
# [12,] -0.87144680 -0.534017411 -0.31190400  0.816298889  0.980932230
# [13,] -0.91423762 -0.355644661  0.16752769  0.561411297  1.031318093
# [14,]  0.96093811  1.015725867  1.10350709 -0.170498169 -0.048449470
# [15,]  0.30569733 -0.546982439 -0.88563856  0.437763728  0.618740572
# [16,]  0.54883989  0.483592318 -1.18173020  0.491095936  1.440611306
# [17,] -0.87820586  1.507868599 -0.65540354  0.460818420  0.816509430
# [18,]  1.22007262  1.986726277  1.08498489 -0.333758241 -0.579086640
# [19,]  1.06667904  1.528796821  1.04530951 -0.181661666 -0.640211428
# [20,]  0.47367378  0.564183541  1.90389483  0.325173793 -0.772635287
# [21,] -0.85902411 -0.343907328 -0.44013035  0.842752338 -0.108462792
# [22,]  1.19611234 -0.577209204  0.68906952  0.452637496 -0.739422910
# [23,]  0.89460669  1.222659484  0.65501500  0.014134844 -0.831633999
# [24,]  1.54114764  0.033502437  1.14627075  0.234381074  0.471306537
# [25,]  1.92292858  0.962156698  1.21765255 -0.108986029 -0.773677567
# [26,]  1.45772199 -1.195033714  1.42043752  0.447899251 -0.594642670
# [27,]  1.54993208 -0.053937157  1.38657624  0.366678809 -1.277450493
# [28,]  1.22030517 -0.275434527 -0.95695728  0.631096484  0.542485653
# [29,]  1.31424340  0.946530346 -1.08777376  0.396487395  0.211119292
# [30,]  1.15668535  0.253675542 -0.73656557  0.479263681  1.048186368
# [31,]  1.03951884 -1.069551242 -1.10482446  0.614338815  2.085611784
# [32,]  0.21426169  0.486112129 -0.97433203  0.160691516  0.807671026
# [33,]  0.72343166  2.497528693 -1.37148960 -0.018601970  1.191001611
# [34,]  0.64275356  0.015014971 -0.74010357  0.415622711 -0.063514599
# [35,]  1.16097600 -0.371169323  2.08180607  0.317773073 -0.795325645
# [36,]  0.51808311  1.110711933  2.20065384 -0.280720289 -0.251853955
# [37,]  1.37039724  3.326166798  1.36030902 -0.503039443 -0.839558330
# [38,]  1.21285912  0.542062574  0.69030436  0.286314342 -1.128700551
# [39,]  1.02143196 -0.945234047  1.51347908  0.385470403 -0.787550471
# [40,]  0.68444444  0.541939618  1.14422497  0.172811355 -0.927267727
# [41,]  0.80652999  0.692789313  1.74826320  0.270994745 -1.152746174
# [42,]  1.22935683  1.305377471  1.29589149 -0.081221023 -0.618636785
# [43,]  1.28453301 -0.395649111  1.96554481 -0.009589968 -0.386301095
# [44,] -1.18144527  0.403947280  0.24019641  0.743458556 -1.040091711
# [45,] -1.00602893 -1.118573267 -0.23301164  0.260914921  0.343436792
# [46,]  0.28395182 -0.992695195  2.16397324 -0.005298199 -0.432810089
# [47,]  0.46935352 -0.144991439  1.83478624  0.170768426 -0.848633519
# [48,]  0.28512312 -1.034731261  1.63624869 -0.098046757 -0.289382285
# [49,]  0.94131884  0.004590750  1.41692477 -0.433965021 -0.609198631
# [50,]  0.15321531 -0.667605970  1.38997787  0.371708166 -0.707973121
# [51,] -0.19492872 -1.316953907 -1.32152134 -1.387317961  2.848772114
# [52,]  0.23694663 -0.161122531  1.50247360  0.532658807 -1.433079495
# [53,] -1.39507175 -0.319061711 -0.72975302 -1.686183076  0.366872700
# [54,] -0.57031958 -1.883675330 -1.15879566 -2.481965252  1.677916021
# [55,] -2.66066014 -0.995918063 -0.40790041 -2.100146394 -0.021622735
# [56,] -1.22417886 -0.955328800 -1.04545755 -1.286698344  2.326397479
# [57,] -1.80685882 -0.456212673  0.28835290  0.119021588 -1.250105471
# [58,] -0.96557946 -1.001002342 -0.32917174 -0.365433006  1.966316405
# [59,] -1.74349451 -1.730272482 -0.71601292 -3.858099787  0.364373439
# [60,] -0.65919189 -0.552171573 -0.33658933 -0.393761962  0.603623490
# [61,] -0.07921936 -0.375778563 -0.89395612 -0.296846327  0.495321740
# [62,] -0.35593996 -1.450371229 -0.41937155 -0.919862587 -0.971792465
# [63,] -0.80009867 -0.079109525 -0.60752386 -0.917662497 -0.645397074
# [64,]  0.65861820  0.052884698 -0.73225661  0.302951778 -0.805732969
# [65,]  0.75414486 -1.224286246 -0.67008136  0.077666665 -0.938192185
# [66,]  0.39115249  0.848365921 -1.04216384 -0.145732763 -0.287584175
# [67,] -1.03557839  3.286493565 -0.79169134  0.062329865 -0.395773429
# [68,] -1.38045341 -0.622164954 -0.61764540 -2.347540749 -0.650349592
# [69,]  1.29123898  0.064751175 -1.03452503  0.434522127 -0.085921121
# [70,] -2.87786572  0.469185378  0.09727047  0.702921070 -0.340501221
# [71,] -0.31853305 -1.296295622 -0.68321191 -0.094224200  1.293203755
# [72,] -0.62033377 -0.176675365 -0.39133568  0.593410628  0.367909362
# [73,] -0.68251182 -0.562687220 -0.43868244  0.398949336  0.137757269
# [74,] -1.43583245  0.785653466 -0.18979208  0.538263476 -0.015535958
# [75,] -2.75926509 -0.057114082 -0.31062410 -3.254925376 -0.786936068
# [76,]  1.52524315  1.045968122 -1.00271429  0.272498913 -0.770981786
# [77,]  0.24362116 -1.424996156 -0.67080577  0.246711853 -0.004253116
# [78,]  0.91146554  1.523635441 -1.19439611 -0.103377739  0.149948492
# [79,]  0.78416949  0.180753104 -0.92150442  0.085719017 -0.520155909
# [80,]  0.97368533  1.085472571 -1.00083079 -0.268960435 -0.227277194
# [81,]  0.54206248  0.010775882 -0.81428063 -0.123671481 -0.216384428
# [82,]  1.03815982 -1.209389165 -0.64751266  0.711474928 -0.982172157
# [83,]  0.51459855 -0.744710351 -0.71844086  0.672919867 -0.086490946
# 
# $loadings
#             [,1]        [,2]        [,3]        [,4]         [,5]
# [1,] -0.93921916  0.27678629  0.19056337  0.07027279  0.002015891
# [2,] -0.14846641 -0.19210171 -0.09662235 -0.96495034 -0.024282003
# [3,]  0.22168438  0.93454616 -0.19067352 -0.20161311  0.021800808
# [4,]  0.21207162  0.10600135  0.94579078 -0.15249441  0.161290425
# [5,] -0.04131301 -0.04328361 -0.15320947  0.00549353  0.986365269
# 
# $prop_expl_var
# [1] 56.40 23.19 14.05  5.65  0.71
# 
# attr(,"class")
# [1] "mgpca"

MDR method

library(plsgenomics)
data(SRBCT)
mydata<-SRBCT$X
mydata<-mydata[,1:5]
groups<-as.factor(SRBCT$Y)
mydata<-split(as.data.frame(mydata),groups)
mdr(g=c(29,11,18,25),grp=groups,data.x=mydata,c=2)

# $variates
#             V1           V2
# 1   3.12202176 -0.821840479
# 2   1.59601843 -0.815421086
# 3   3.19351655 -0.675033314
# 4   0.96173934 -0.248191188
# 5   2.62641826 -0.186473588
# 6   1.99336399 -0.697375665
# 7   1.76629017 -0.763485594
# 8   2.62973615 -0.321697736
# 9   2.28264534 -0.590075377
# 10  1.86028044 -0.336384244
# 11  3.51718635 -0.441444760
# 12  2.08399635 -0.366983036
# 13  2.19519126 -0.428479665
# 14  0.81774008 -1.400475271
# 15  0.87611500 -0.529004301
# 16  0.87157853 -1.176914092
# 17  2.51859002 -1.489369550
# 18  0.79927593 -1.964447242
# 19  0.84147391 -1.694077685
# 20  1.31135152 -1.071361224
# 21  2.11366050 -0.458186627
# 22  0.22782228 -0.590485766
# 23  0.90382926 -1.515588029
# 24  3.05356781 -2.408330961
# 25  4.24802863 -0.554183285
# 26  1.90789878 -0.579941444
# 27  1.84484902 -0.333574180
# 28  2.92707061 -0.969156826
# 29  0.68099806 -0.452015376
# 30  0.07902264 -0.986420975
# 31 -0.06985239 -1.514802041
# 32 -0.08656825 -0.270430892
# 33  0.10102938 -0.906384146
# 34  0.10277898 -0.847239929
# 35  0.27888174 -1.526406320
# 36  0.29923080 -1.126845238
# 37  0.04741245 -0.406547431
# 38  0.09384939 -1.022781851
# 39  0.10817210 -1.583933587
# 40  0.09437601 -0.259207594
# 41  1.17583097 -1.078191735
# 42  1.13121560 -2.295174559
# 43  0.71875988 -0.880029695
# 44  0.45768545 -0.653024251
# 45  1.37024418 -1.340190390
# 46  1.00538890 -2.715296664
# 47  0.47357144 -1.200251812
# 48  0.38764563 -0.327760965
# 49  1.00568606 -1.097142484
# 50  1.01066255 -1.189705730
# 51  0.67397690 -1.597442927
# 52  0.28474238 -0.644696642
# 53  0.70601123 -0.878932571
# 54  1.06511637 -1.264522535
# 55  0.73125839 -1.745627267
# 56  0.57328484 -0.964640487
# 57  0.57087070 -1.483461202
# 58  0.74497419 -0.816276902
# 59  2.67267029 -0.780445452
# 60  2.01664477  0.043711589
# 61  1.09467821 -0.139665161
# 62  1.11523969 -0.659996537
# 63  1.01141553 -0.125191926
# 64  0.59592249 -0.788236205
# 65  1.25092103 -0.345112431
# 66  0.89036181  0.074664639
# 67  1.33282685 -0.638146291
# 68  2.30740446 -0.197582836
# 69  1.00584282  0.571725222
# 70  3.31532714  0.439825462
# 71  1.98670759  0.050155344
# 72  2.98186403 -0.138733308
# 73  1.91933878 -0.015127747
# 74  2.04687561  0.827889538
# 75  1.74805569 -0.286574117
# 76  1.19721947 -0.500400564
# 77  1.18396499  0.241875198
# 78  1.91516519 -0.467418666
# 79  0.28362805 -0.154640916
# 80  2.16479920  0.047981812
# 81  1.23465926  0.028026774
# 82  3.52898464  0.040489155
# 83  0.72383697  0.008385486
# 
# $loadings
#             [,1]         [,2]
# [1,]  0.98614287 -0.002436152
# [2,] -0.06903002  0.560697342
# [3,] -0.02923694 -0.819796115
# [4,] -0.14390561 -0.109894629
# [5,]  0.03454657  0.038341319
# 
# $prop_expl_dim
# [1] 66.78 25.87  7.36  0.00  0.00
# 
# attr(,"class")
# [1] "mdr"