tcga data variance analysis

Omit omit value is indicated when making volcano image. Then na.omit is used to remove missing value, but all original data is deleted(omitted 59177 rows). Don't know why

#volcano
> pdf(file="vol.pdf")
> xMax=max(-log10(allDiff$FDR))+1
> yMax=12
> na.omit(allDiff)
          logFC       logCPM        PValue           FDR
51158 -4.085450  5.548859136 6.214568e-226 3.693131e-221
54294 -3.068080  4.204435273 1.430167e-209 3.277513e-205
27795 -4.545381  5.278036354 1.654558e-209 3.277513e-205
42645 -2.125593  4.644799803 3.648711e-206 5.420798e-202
54941 -3.257860  4.426281437 2.141086e-195 2.544766e-191
53647 -2.731234  0.606070423 2.080700e-194 2.060830e-190
27444 -2.711526  9.273417495 7.869608e-194 6.680960e-190
45878 -2.887637  6.259518865 6.966081e-192 5.174666e-188
51682 -3.221780  4.017477616 2.097395e-191 1.384910e-187
51265 -2.856098  5.330517770 4.685079e-191 2.784202e-187
45416 -3.227206  4.655161281 4.718192e-183 2.548982e-179
27358 -2.728559  8.363518127 6.827515e-183 3.381156e-179
26903 -3.505026  5.109836763 2.079885e-179 9.507794e-176
52605 -6.155536  4.634446977 9.069316e-178 3.849730e-174
43257 -2.318046  8.079549582 3.505774e-174 1.388918e-170
45067 -2.454466  4.713159210 5.727690e-174 2.127372e-170
28355 -4.526766  5.095196028 1.822127e-173 6.369620e-170
13646 -2.567637  5.662349274 3.905061e-173 1.289256e-169
33629 -2.607915  4.475531731 7.971589e-172 2.493303e-168
42817 -2.517210  7.115768734 7.775235e-170 2.310294e-166
44797 -3.346950  4.671460063 2.033043e-169 5.753220e-166
45414 -2.870141  4.384292894 1.187526e-165 3.172878e-162
18985 -5.230552 -1.412877182 1.227997e-165 3.172878e-162
31295 -2.787805  3.288503678 1.344621e-165 3.329450e-162
9259  -3.329523  1.363402827 2.699133e-164 6.416055e-161
18653 -3.632164 -0.431873054 5.439386e-163 1.243255e-159
57999 -2.369477  5.498258902 1.047391e-162 2.305307e-159
19569 -4.230259  0.337655203 7.871054e-161 1.670547e-157
33775 -2.812375  4.778009028 5.304102e-157 1.086920e-153
27747 -4.902531  4.443574437 4.108329e-156 8.138189e-153
14025 -5.025299  8.319331361 5.681221e-156 1.089090e-152
49604 -2.845997  4.861286051 1.088560e-154 2.021559e-151
53839 -3.200176  7.157484414 5.288969e-153 9.524471e-150
32531 -2.518228  4.016460633 1.770362e-152 3.094333e-149
23037 -2.753524  5.797984518 2.313730e-152 3.928516e-149
54626 -2.810488  2.094485208 8.435457e-151 1.392483e-147
40311 -3.299812  1.574449684 6.708576e-150 1.058838e-146
28488 -3.430292  6.128317404 6.770637e-150 1.058838e-146
23230 -3.313473  6.159945404 1.214703e-149 1.850926e-146
23608 -2.773507  2.481487861 4.917614e-149 7.305976e-146
32579 -2.862562  2.637049360 2.269254e-147 3.289145e-144
23801 -2.552108  6.151001002 4.440497e-147 6.282986e-144
24528 -3.772780  3.346494096 5.422697e-147 7.343261e-144
28600 -3.277983  5.821520446 5.436981e-147 7.343261e-144
55380 -4.372747  4.684907994 5.323364e-145 7.030034e-142
28702 -2.752198  3.757643518 2.036222e-142 2.630578e-139
43739 -2.737061  2.703616011 3.766484e-141 4.762358e-138
28393 -3.913189  3.420340571 6.289494e-141 7.786786e-138
52724 -2.580131  4.283699586 1.657916e-140 2.010714e-137
51925 -3.838968  0.006072789 8.569224e-139 1.018487e-135
30192 -3.310512 -0.182822556 4.652930e-138 5.421758e-135
21182 -2.691622  4.669910873 9.015843e-136 1.030355e-132
44584 -1.894444  4.552470544 4.846369e-135 5.434059e-132
29422 -2.461602  4.632072489 6.764756e-135 7.444613e-132
13849 -3.095456  3.316780864 1.308027e-134 1.413311e-131
34222 -3.540757  0.711174877 4.633054e-134 4.916581e-131
25746 -2.281266  4.141982336 7.807899e-134 8.140351e-131
51957 -2.296808  4.668709787 1.215021e-132 1.244915e-129
33523 -3.644121  0.362412661 5.329254e-132 5.367823e-129
23226 -3.412493  8.164901122 7.703076e-132 7.629512e-129
29971 -2.497767  5.041486939 1.244051e-129 1.211971e-126
54142 -3.557054  2.570207036 2.049964e-129 1.964891e-126
57594 -3.232229  4.728705338 4.257254e-129 4.015807e-126
36368 -3.201702  3.838434496 1.069273e-128 9.928697e-126
23501 -2.543741  1.304001209 3.431304e-128 3.137109e-125
29768 -3.946733  3.672219796 9.643883e-127 8.683440e-124
29779 -4.465525  3.236130277 6.363543e-126 5.644273e-123
28423 -2.250192  4.803747250 7.839656e-126 6.851283e-123
7977  -3.624787 -0.293098180 5.479313e-125 4.719118e-122
54167 -2.026535  4.235882630 2.011710e-123 1.707856e-120
30448 -4.167941  4.434438630 1.699676e-122 1.422629e-119
40192 -2.267986  3.527097939 3.283421e-122 2.710054e-119
30450 -4.258867  6.967149167 5.183324e-122 4.219581e-119
21173 -2.454127  3.848074403 6.561082e-122 5.268992e-119
24520 -2.298076  2.090453180 1.210148e-121 9.588732e-119
40716 -3.235630  2.145550239 5.990417e-121 4.684112e-118
32248 -3.530739  5.735507257 8.662462e-121 6.685508e-118
53626 -2.938920  2.777122087 1.228315e-120 9.358346e-118
24553 -3.629500  6.285939319 3.763219e-119 2.830846e-116
55786 -3.575597  3.869514877 8.958000e-119 6.654338e-116
36142 -2.361728  5.539537219 1.262055e-118 9.259274e-116
57328 -2.319100  1.666972405 1.907062e-118 1.382085e-115
25274 -2.389631  6.187960395 2.008637e-118 1.438160e-115
45079 -2.588074  5.685611919 2.944827e-118 2.083360e-115
51516 -3.578240  3.031081156 5.532052e-118 3.867685e-115
54178 -2.214122  3.994010390 5.823562e-118 4.024149e-115
51218 -3.095472  1.220971422 2.089894e-117 1.427541e-114
27532 -2.153172  4.501487081 6.524811e-117 4.406249e-114
20205 -3.076491 -0.445104891 8.937815e-117 5.967950e-114
24513 -2.300531  5.108230958 1.027512e-116 6.784661e-114
27339 -2.754738  4.391724427 1.151704e-116 7.521134e-114
21162 -2.375664  2.688316194 2.185257e-116 1.411557e-113
30447 -4.382206 -0.986861368 4.273731e-116 2.730914e-113
23657 -4.968834  1.492404379 4.412514e-116 2.789601e-113
41117 -2.419702  2.594478569 7.069779e-116 4.422482e-113
54321 -3.502148  3.112466621 7.262276e-116 4.495576e-113
54629 -2.360720  3.686446059 1.673868e-115 1.025494e-112
36745 -4.040092  4.173730622 1.111981e-114 6.743029e-112
52515 -2.504275  7.537483597 1.177902e-114 7.070625e-112
22742 -2.575382 -1.042199472 5.313279e-114 3.157522e-111
55181 -2.245871  2.629713869 1.699917e-113 1.000207e-110
26878 -2.259502  0.097784076 4.183165e-113 2.437186e-110
29776 -3.706814  3.227068590 1.077731e-110 6.218092e-108
19390 -4.094408 -0.836145705 1.862560e-110 1.064292e-107
19758 -2.654481  6.369314336 7.899511e-110 4.470898e-107
2584  -4.169032  1.587059546 1.816917e-109 1.018622e-106
53613 -2.719373  1.943775440 2.525061e-109 1.402400e-106
39146 -2.135617  4.983790306 1.700534e-108 9.357187e-106
22578 -2.642414  4.636125776 3.305876e-108 1.802370e-105
12476 -4.054677 -1.976508312 3.376780e-108 1.824290e-105
22366 -3.439351  3.695922497 7.508923e-108 4.020115e-105
51356 -1.868571  5.469967985 8.343086e-108 4.426827e-105
30631 -2.796642 -1.771351441 1.748367e-107 9.194708e-105
30656 -2.756169  1.623472170 7.963551e-107 4.151315e-104
23706 -2.213797  6.999996212 2.403208e-106 1.241873e-103
22947 -4.360113  2.852556381 3.100623e-106 1.588454e-103
28820 -4.308220 -0.833263202 4.460595e-106 2.265639e-103
55813 -2.180547  8.438310504 5.409405e-106 2.724277e-103
57971 -4.109184  1.342947246 9.119457e-106 4.554134e-103
23683 -4.057487 -0.902105878 3.692707e-105 1.828721e-102
40538 -3.540413  3.612235085 4.706700e-105 2.311612e-102
19720 -2.804046  5.803165287 1.099056e-104 5.353576e-102
37792 -3.388090 -0.793419888 2.259823e-104 1.091825e-101
24536 -4.468160 -1.329185593 1.059298e-103 5.076687e-101
18107 -3.432527 -2.888645124 3.736452e-103 1.776369e-100
52691 -2.491666  5.248322000 4.408253e-103 2.079121e-100
27008 -2.595038  2.735105749 6.455062e-103 3.020512e-100
45510 -2.317875  3.948617518 9.133786e-103 4.240574e-100
23212 -1.913842  6.998934408 1.349101e-102 6.214964e-100
43207 -1.982392  4.476399335 1.455919e-102 6.655452e-100
42664 -3.911701 -0.505992854 1.924666e-102 8.731076e-100
35998 -1.929512  3.944821471 1.180190e-101  5.300408e-99
34097 -3.490642 -2.389019944 1.186253e-101  5.300408e-99
41042 -2.689801  0.827314563 2.406605e-101  1.067293e-98
9536  -2.754697 -1.315946833 1.249115e-100  5.473789e-98
19600 -4.454168  3.686161812 1.252689e-100  5.473789e-98
32578 -1.644636  6.726127154 1.471722e-100  6.383945e-98
28408 -2.151450  3.330886429 6.587150e-100  2.836627e-97
53889 -1.756748  8.938338093 6.673462e-100  2.853121e-97
51692 -2.580034  3.682636984 7.685234e-100  3.262217e-97
40284 -4.558260 -0.336025090 8.364228e-100  3.525255e-97
32559 -2.608011  0.830514045  1.947728e-99  8.151240e-97
21142 -2.147707  5.767756222  2.405345e-99  9.995976e-97
15085 -2.521759 -1.596030337  2.398537e-98  9.898463e-96
30551 -2.131196  6.750717933  6.039358e-98  2.475179e-95
54963 -2.811060  3.299147497  6.167379e-98  2.510334e-95
26080 -1.769085  5.874289945  1.629605e-97  6.587929e-95
30454 -2.576114  5.364485699  4.662555e-97  1.872173e-94
55804 -3.877647  0.603442709  4.851384e-97  1.934921e-94
51487 -2.824278  3.341387042  6.222649e-97  2.465289e-94
13719 -3.533561  3.403373856  6.828903e-97  2.687558e-94
25224 -4.685653  3.316816610  1.606972e-96  6.282731e-94
10354 -2.954924 -1.312923566  2.341103e-96  9.093121e-94
28491 -2.790491  1.931407527  3.588502e-96  1.384765e-93
52115 -2.790488  3.165300968  9.768290e-96  3.745163e-93
7983  -2.492704 -0.654381623  4.294202e-95  1.635843e-92
29492 -2.218997  5.657846833  4.456654e-95  1.686914e-92
55091 -2.596005  4.670315283  1.763877e-94  6.634299e-92
35082 -4.869223 -0.960074452  1.851119e-94  6.883835e-92
27918 -2.870059  4.487013406  1.853389e-94  6.883835e-92
45957 -1.882233  3.835013401  2.008150e-94  7.412320e-92
21080 -3.456612  1.393967032  4.512210e-94  1.655229e-91
29420 -2.099311  4.982785254  5.123480e-94  1.867933e-91
28848 -2.449149  2.498670540  1.328727e-93  4.814773e-91
40983 -2.092878  2.615084416  1.670051e-93  6.014916e-91
34296 -3.748118 -3.529703268  1.993132e-93  7.135291e-91
24192 -2.232088  5.691102322  2.688307e-93  9.566349e-91
57273 -4.165470  4.824665721  3.636098e-93  1.286205e-90
29807 -2.107195  0.161985999  5.649518e-93  1.986591e-90
43249 -1.668016  5.870968675  1.214107e-92  4.244160e-90
42363 -4.076932 -3.230420263  2.063763e-92  7.172120e-90
26436 -3.487379  2.412583439  2.863201e-92  9.892526e-90
13733 -1.777849  4.860116247  3.369560e-92  1.157473e-89
35064 -4.434300 -0.630398112  4.736233e-92  1.617587e-89
9584  -4.499685 -2.878047205  6.511065e-92  2.211046e-89
43266 -2.541626  4.235799520  8.992579e-92  3.036375e-89
26544 -3.260403  0.022343665  1.984785e-91  6.663832e-89
55138 -2.434213  6.017514890  2.048889e-91  6.840412e-89
29414 -2.048279  3.046980600  2.125244e-91  7.055690e-89
54849 -3.117237  2.688283242  2.357018e-91  7.781695e-89
7878  -4.166465 -3.321598554  1.895239e-90  6.222561e-88
27800 -2.318316  1.254073708  2.126817e-90  6.944524e-88
23229 -2.068393  8.039933887  2.772485e-90  9.003303e-88
40594 -1.600293  6.975547210  6.370053e-90  2.057354e-87
55505 -1.921703  4.507982504  2.998855e-89  9.633133e-87
30054 -2.459850  2.184644135  7.939932e-89  2.536808e-86
36283 -2.229352  7.127530445  8.734266e-89  2.775675e-86
54057 -3.895485 -3.247369994  1.296934e-88  4.099623e-86
54558 -1.857170  7.080100077  1.662645e-88  5.227831e-86
24635 -2.330131 -0.929844895  3.961443e-88  1.239035e-85
45166  3.684490  6.374406931  1.385609e-87  4.311129e-85
44329 -1.871531  6.782193278  1.400524e-87  4.334841e-85
22098 -1.360117  7.007526242  1.517060e-87  4.671208e-85
32538 -2.098874  6.010200739  7.850249e-87  2.404726e-84
35982 -1.764165  5.401356877  8.424488e-87  2.567395e-84
41560 -2.424588  1.962217578  2.174685e-86  6.593624e-84
42372 -4.161413 -3.241624925  2.237257e-86  6.748908e-84
32983 -1.800280  7.833149763  4.497245e-86  1.349787e-83
10564 -4.062654 -2.456173289  5.797610e-86  1.731330e-83
22522 -3.798098  0.234831779  5.992106e-86  1.780464e-83
52547 -3.406292 -1.988605046  9.566870e-86  2.828509e-83
41240 -2.624275  4.430601516  1.492081e-85  4.389598e-83
20207 -2.485880 -0.517779740  1.620481e-85  4.743859e-83
13838 -1.610518  4.273688845  1.859546e-85  5.417021e-83
12202 -4.286921 -2.710662574  2.223911e-85  6.446848e-83
5988  -3.348627  0.174889420  2.984968e-85  8.611053e-83
20311 -2.416775  1.027915270  3.764554e-85  1.080754e-82
51980 -4.240881 -0.035038669  4.726401e-85  1.350364e-82
10561 -4.137794 -3.077589740  5.263913e-85  1.496740e-82
4633  -2.494198 -0.918965267  6.896818e-85  1.951701e-82
24313 -4.478655 -0.590592284  7.245948e-85  2.040782e-82
12074 -2.150725  1.823954818  8.138303e-85  2.281297e-82
56772 -2.687234 -0.280101605  8.595817e-85  2.398233e-82
53832 -2.289873  5.086859388  8.774339e-85  2.436601e-82
23448 -2.772703  0.539786951  2.585556e-84  7.146597e-82
34024 -2.658383 -0.259651604  5.423985e-84  1.492274e-81
45702 -1.818730  5.606059152  9.308978e-84  2.549330e-81
23183 -1.715962  5.400384638  1.579802e-83  4.306554e-81
43956 -1.576381  6.314926827  1.837889e-83  4.987224e-81
13773 -2.883997  0.629972340  2.342523e-83  6.327687e-81
21432 -2.651977  0.907007711  2.418783e-83  6.504119e-81
27729 -1.817874  4.487136991  3.370070e-83  9.021313e-81
53398 -1.197653  5.004633206  3.767057e-83  1.003879e-80
23874 -2.707230  1.599429694  1.273005e-82  3.377271e-80
33651 -2.109211  7.066209542  1.618289e-82  4.274226e-80
17190 -2.540276 -1.762522498  2.613412e-82  6.872003e-80
51828 -1.640783  4.462422864  6.286784e-82  1.645836e-79
13698 -2.356942  5.885962689  6.982791e-82  1.820028e-79
57783 -2.323754  8.230638346  7.269622e-82  1.886515e-79
45395 -2.135318  3.779035706  7.419262e-82  1.916976e-79
24500 -2.719259  5.381737494  8.967602e-82  2.307003e-79
33510 -2.788625  7.453934466  9.864971e-82  2.526921e-79
32160 -1.742342  3.796660940  1.085073e-81  2.767496e-79
33730 -1.717131  5.169401241  7.493025e-81  1.902940e-78
30457 -3.859059 -3.953382423  1.471208e-80  3.720404e-78
41113 -1.841121  4.836984422  2.212088e-80  5.570243e-78
45074 -3.414852 -0.852277614  4.270205e-80  1.070740e-77
40165 -1.974484  6.961168178  4.630820e-80  1.156285e-77
52236 -2.926764  2.768358108  9.449885e-80  2.349700e-77
55206 -1.973501  5.139394179  1.071148e-79  2.652296e-77
51689 -2.529281  5.100456967  1.230047e-79  3.033111e-77
33809 -3.414219 -2.063970250  2.251712e-79  5.529441e-77
37027 -3.025464  3.999790266  4.656260e-79  1.138714e-76
57566 -3.592129  3.402279421  8.843038e-79  2.153751e-76
150   -2.521433  5.426700226  9.190097e-79  2.229142e-76
54497 -1.830737  3.740031458  1.385059e-78  3.345932e-76
26517 -2.189851  2.523392216  1.040205e-77  2.502681e-75
19456 -3.063353  0.674605448  1.829837e-77  4.384747e-75
23187 -2.522518 -1.266539614  4.206564e-77  1.003950e-74
23662 -2.913317  5.620988901  5.551323e-77  1.319594e-74
 [ reached 'max' / getOption("max.print") -- omitted 59177 rows ]
> plot(-log10(allDiff$FDR), allDiff$logFC, xlab="-log10(FDR)",ylab="logFC",
+      main="Volcano", xlim=c(0,xMax),ylim=c(-yMax,yMax),yaxs="i",pch=20, cex=0.4)
> diffSub=allDiff[allDiff$FDR<padj & allDiff$logFC>foldChange,]
> points(-log10(diffSub$FDR), diffSub$logFC, pch=20, col="red",cex=0.4)
> points(-log10(diffSub$FDR), diffSub$logFC, pch=20, col="red",cex=0.4)
> diffSub=allDiff[allDiff$FDR<padj & allDiff$logFC<(-foldChange),]
> diffSub=allDiff[allDiff$FDR<padj & allDiff$logFC<(-foldChange),]
> points(-log10(diffSub$FDR), diffSub$logFC, pch=20, col="green",cex=0.4)
> abline(h=0,lty=2,lwd=3)
> dev.off()