hahahueg 2023-02-28 18:13 采纳率: 87.5%
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已结题

tcga数据差异分析

绘制火山图时提示xlim不能为无限值,然后使用na.omit去除缺失值,但是把原始数据全部删除了(omitted 59177 rows),不知道为什么


#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()
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2条回答 默认 最新

  • 社区专家-Monster-XH 2023-02-28 18:16
    关注

    基于Monster 组和GPT的调写:
    在R中使用na.omit()函数时,它会删除包含缺失值的行并返回一个不包含缺失值的数据框。在您的代码中,您没有将结果赋值给新的对象,所以原始数据框被改变并且删除了所有行。

    要避免这种情况,请将结果保存在新的数据框中,例如:

    allDiff_noNA <- na.omit(allDiff)
    
    
    

    然后使用allDiff_noNA来绘制火山图。

    本回答被题主选为最佳回答 , 对您是否有帮助呢?
    评论
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