[BioC] Why the resuts are so different between the classic and the glm methods?

Jiantao Yu joelyu.2003 at gmail.com
Thu Dec 12 22:54:05 CET 2013


Dear Sir/Madam,

When I used edgeR to do RNA-Seq analysis, I found the datasets of the
resulting DEGs generated by 'Classic' and 'GLM' methods are very different,
the former contain ~460 DEGs, whereas the latter generate ~27,000 DEGs. I
don't know why this was happening. I attached the scripts and the source
data I used, hope you would help me to explain this.

Joel
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"mu1.bam" "mu2.bam" "mu3.bam" "wt1.bam" "wt2.bam" "wt3.bam"
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"ATCG00520" 46286 47609 41189 47207 39488 34548
"ATCG00530" 58653 64550 48273 71378 53025 45296
"ATCG00540" 94121 96781 91820 111020 108528 74275
"ATCG00550" 59509 60151 63963 30247 29557 21778
"ATCG00560" 65567 104700 91726 44854 48512 58755
"ATCG00570" 65668 102931 82867 42528 48395 58811
"ATCG00580" 122933 189836 152004 81365 91456 116655
"ATCG00590" 9802 13076 3656 13788 1955 3978
"ATCG00600" 10156 12939 7233 13406 7944 7500
"ATCG00610" 4291 6422 4345 6214 5843 4812
"ATCG00620" 5848 9304 6762 8434 8725 7981
"ATCG00630" 55494 39391 39591 42186 35172 20885
"ATCG00640" 20576 28919 21872 24674 25896 19394
"ATCG00650" 13332 20765 12477 18964 12123 16148
"ATCG00660" 7935 11153 9380 5545 5920 3311
"ATCG00670" 92985 104329 89406 122861 112838 63580
"ATCG00680" 453669 544481 412940 198413 260726 311391
"ATCG00690" 13024 24758 13034 9115 9141 10123
"ATCG00700" 22952 12797 10770 8618 11149 10213
"ATCG00710" 58242 43643 41687 28772 33344 43486
"ATCG00720" 235738 255818 184584 134076 135782 194851
"ATCG00730" 209687 258976 207841 118539 121972 166293
"ATCG00740" 32874 42910 32597 36013 35948 28792
"ATCG00750" 19792 21127 17924 20026 20842 16353
"ATCG00760" 6645 8292 7421 8273 8344 4732
"ATCG00770" 16521 19822 17410 17261 20297 12852
"ATCG00780" 25360 27885 22600 26739 25162 16972
"ATCG00790" 56093 63060 47034 50996 48054 32006
"ATCG00800" 30540 28618 24192 27084 28475 24113
"ATCG00810" 16832 16661 13828 13795 14589 12279
"ATCG00820" 9074 10190 9111 6865 8076 7702
"ATCG00830" 58481 67995 55965 37252 44043 41343
"ATCG00840" 11362 10529 7600 6202 7022 6938
"ATCG00850" 884 712 701 972 1105 711
"ATCG00860" 90036 94078 83407 94116 97965 78515
"ATCG00870" 1685 2594 2093 2790 3018 1605
"ATCG00880" 243 846 1044 1290 1903 632
"ATCG00890" 106170 125614 105649 102570 101316 81998
"ATCG00900" 7030 8180 8114 7466 8386 6185
"ATCG00905" 24898 29389 25772 23215 23805 14796
"ATCG00910" 392 220 211 348 545 3
"ATCG00920" 22299 1565 3212 1974 2459 9
"ATCG00930" 246790 205987 222659 205626 237380 122420
"ATCG00940" 145001 114630 110664 39150 50888 178446
"ATCG00950" 3345 14 0 0 0 2
"ATCG00960" 3345 14 0 0 0 2
"ATCG00970" 3345 14 4 2 0 5
"ATCG00980" 3349 18 4 2 4 6
"ATCG00990" 4864 1223 1967 1832 2357 1267
"ATCG01000" 49415 64016 46907 71741 64514 40931
"ATCG01010" 47060 64614 33052 66759 38228 27574
"ATCG01020" 26789 27113 19054 38820 21296 15627
"ATCG01030" 3769 77 54 97 75 65
"ATCG01040" 18206 21435 13256 15844 13725 6274
"ATCG01050" 110287 137608 102430 147996 114999 78115
"ATCG01060" 62821 70496 54578 102668 70884 55593
"ATCG01070" 38534 38636 27377 45710 34371 26311
"ATCG01080" 44819 53123 37966 61588 46638 26007
"ATCG01090" 29074 33458 22560 38728 27712 20034
"ATCG01100" 115117 136016 101016 165540 122509 74409
"ATCG01110" 23182 19479 16010 18262 15619 12508
"ATCG01120" 6865 3275 2560 2295 2076 1525
"ATCG01130" 81370 103350 74498 107551 86036 64886
"ATCG01140" 4864 1209 1967 1832 2357 1267
"ATCG01150" 3349 4 4 2 4 6
"ATCG01160" 3345 0 4 2 0 5
"ATCG01170" 3345 0 0 0 0 2
"ATCG01180" 3345 0 0 0 0 2
"ATCG01190" 145001 114617 110664 39150 50888 178446
"ATCG01200" 246790 205974 222659 205626 237265 122420
"ATCG01210" 22299 1552 3212 1974 2308 9
"ATCG01220" 392 207 211 348 394 3
"ATCG01230" 24898 29376 25772 23215 23654 14796
"ATCG01240" 7030 8167 8114 7466 8235 6185
"ATCG01250" 106170 125601 105649 102570 101165 81998
"ATCG01260" 243 833 1044 1290 1752 632
"ATCG01270" 1685 2581 2093 2790 2867 1605
"ATCG01280" 90036 94065 83407 94110 97813 78515
"ATCG01290" 884 699 701 966 953 711
"ATCG01300" 11362 10516 7600 6196 6870 6938
"ATCG01310" 58481 67982 55965 37246 43891 41343
"ATMG00010" 31 36 29 32 30 25
"ATMG00020" 1 2 0 0 0 0
"ATMG00030" 33 30 23 40 43 14
"ATMG00040" 7485 6891 5382 6749 7447 3477
"ATMG00050" 370 374 338 183 186 582
"ATMG00060" 12638 14780 11626 14719 12643 12154
"ATMG00070" 7104 8443 6625 9151 7350 7643
"ATMG00080" 3412 4398 2926 770 905 2696
"ATMG00090" 10566 11501 8555 3492 4328 10589
"ATMG00100" 68 29 21 41 33 42
"ATMG00110" 876 1126 755 1181 810 677
"ATMG00120" 46 29 20 30 38 36
"ATMG00130" 79 73 65 75 80 80
"ATMG00140" 100 80 67 95 78 101
"ATMG00150" 66 50 26 51 55 26
"ATMG00160" 17654 21014 15910 25257 21039 14112
"ATMG00170" 94 117 107 121 131 92
"ATMG00180" 5094 6337 5209 4395 3791 4251
"ATMG00190" 71 61 66 60 71 78
"ATMG00200" 210 182 160 62 111 257
"ATMG00210" 2313 3287 2206 437 700 2372
"ATMG00220" 17631 20805 15040 16618 15941 14709
"ATMG00230" 10 5 7 1 14 15
"ATMG00240" 20 21 15 14 15 11
"ATMG00250" 22 14 19 11 17 17
"ATMG00260" 69 63 48 51 62 58
"ATMG00270" 9512 12607 10944 13130 10885 6755
"ATMG00280" 333799 363804 274831 246772 258495 353364
"ATMG00285" 4096 4423 3699 3654 3399 3152
"ATMG00290" 2608 2501 1954 962 1225 1960
"ATMG00300" 222 206 150 108 113 154
"ATMG00310" 163 148 102 73 68 95
"ATMG00320" 140 115 87 60 59 86
"ATMG00330" 179 226 520 409 1063 245
"ATMG00340" 58 25 30 28 28 45
"ATMG00350" 70 34 45 18 25 36
"ATMG00360" 127 82 98 110 130 72
"ATMG00370" 6611 7499 5512 7689 7741 5513
"ATMG00380" 284 238 406 440 524 346
"ATMG00390" 76 25 49 3 9 37
"ATMG00400" 720 681 536 402 428 497
"ATMG00410" 34401 38386 28834 41192 33932 26722
"ATMG00420" 220 257 242 368 174 168
"ATMG00430" 85 63 71 26 49 91
"ATMG00440" 103 75 57 31 39 69
"ATMG00450" 86 80 56 30 53 69
"ATMG00460" 65 40 39 18 29 40
"ATMG00470" 55 37 38 11 20 51
"ATMG00480" 14094 14814 13555 19226 17094 11410
"ATMG00490" 764 632 539 361 404 1251
"ATMG00500" 1104 1054 816 480 512 1549
"ATMG00510" 12383 14277 9559 7639 7183 13717
"ATMG00513" 13646 14091 10181 10177 9394 9650
"ATMG00516" 16626 16764 14015 7356 8393 13737
"ATMG00520" 5771 6363 4926 1946 2735 5345
"ATMG00530" 200 124 110 31 47 152
"ATMG00540" 65 50 41 32 23 82
"ATMG00550" 52 45 23 7 17 36
"ATMG00560" 5252 5388 4537 4326 4910 3926
"ATMG00570" 1511 1670 1226 1955 1670 1165
"ATMG00580" 27248 31715 25702 27916 25520 21616
"ATMG00590" 1870 2121 1816 1740 1583 1550
"ATMG00600" 97 103 39 37 55 54
"ATMG00610" 615 454 422 542 514 469
"ATMG00620" 124 140 125 124 136 112
"ATMG00630" 59 66 44 44 39 56
"ATMG00640" 3385 4479 3326 533 728 4893
"ATMG00650" 2808 3526 2311 1132 915 2870
"ATMG00660" 1591 1723 1565 236 473 2047
"ATMG00665" 130 101 102 51 87 118
"ATMG00670" 1174 1003 941 795 888 1225
"ATMG00680" 44 31 26 6 11 44
"ATMG00690" 3032 2641 2611 2264 2382 2349
"ATMG00700" 86 51 37 46 31 64
"ATMG00710" 72 74 48 17 19 70
"ATMG00720" 41 34 27 11 16 37
"ATMG00730" 15760 19214 14282 15065 16727 12219
"ATMG00740" 67 54 51 38 29 56
"ATMG00750" 58 44 35 20 20 43
"ATMG00760" 70 48 40 38 28 55
"ATMG00770" 56 40 29 25 23 41
"ATMG00780" 151 236 520 414 1065 242
"ATMG00790" 57 38 30 34 31 43
"ATMG00800" 37 22 19 7 7 26
"ATMG00810" 350 311 302 289 298 308
"ATMG00820" 144 124 97 53 73 116
"ATMG00830" 983 1047 931 175 287 1080
"ATMG00840" 52 38 27 7 14 42
"ATMG00850" 44 30 27 11 9 58
"ATMG00860" 47 31 25 12 14 40
"ATMG00870" 65 47 34 18 16 64
"ATMG00880" 62 40 36 13 16 54
"ATMG00890" 58 43 36 31 29 55
"ATMG00900" 565 864 479 377 303 754
"ATMG00910" 94 92 59 35 38 158
"ATMG00920" 460 535 427 654 519 371
"ATMG00930" 1588 2527 1628 2777 2231 2256
"ATMG00940" 99 123 59 59 70 67
"ATMG00950" 50 31 23 21 17 34
"ATMG00960" 593 759 638 62 59 577
"ATMG00970" 230 213 140 62 65 168
"ATMG00980" 731 972 714 314 383 452
"ATMG00990" 807 939 722 389 464 650
"ATMG01000" 633 559 605 263 263 563
"ATMG01010" 478 309 365 158 145 430
"ATMG01020" 551 366 330 187 151 463
"ATMG01030" 93 74 70 49 50 78
"ATMG01040" 176 278 212 117 111 312
"ATMG01050" 137 132 98 84 90 96
"ATMG01060" 128 60 133 79 185 82
"ATMG01070" 101 41 112 48 148 61
"ATMG01080" 27518 20621 19316 23453 25647 14677
"ATMG01090" 1578 1702 1505 796 815 2849
"ATMG01100" 63 35 35 11 16 45
"ATMG01110" 138 92 104 114 106 132
"ATMG01120" 3125 2990 2683 691 612 2673
"ATMG01130" 1355 1445 1284 35 45 1803
"ATMG01140" 72 55 39 25 28 45
"ATMG01150" 54 43 53 20 38 67
"ATMG01160" 358 469 432 792 345 297
"ATMG01170" 24381 28846 22442 33361 27146 20181
"ATMG01180" 36 17 16 7 6 27
"ATMG01190" 52384 59850 45512 42023 47336 46616
"ATMG01200" 7668 7039 6000 4898 5918 6472
"ATMG01210" 320 514 376 536 451 423
"ATMG01220" 481 622 468 630 699 494
"ATMG01230" 75 57 34 35 39 49
"ATMG01240" 46 38 42 25 20 31
"ATMG01250" 43 49 27 28 21 31
"ATMG01260" 73 99 69 33 37 49
"ATMG01270" 344 477 334 35 53 410
"ATMG01275" 1414 1641 1297 1076 862 1777
"ATMG01280" 5275 5763 5211 6820 6359 6493
"ATMG01290" 26 27 29 23 16 25
"ATMG01300" 21 19 8 6 4 23
"ATMG01310" 12 16 11 10 10 19
"ATMG01320" 11827 14464 11211 9855 9549 11458
"ATMG01330" 699 866 734 548 499 866
"ATMG01340" 17 21 16 13 12 19
"ATMG01350" 302 368 323 243 286 222
"ATMG01360" 40177 47605 37614 56036 49521 34581
"ATMG01370" 60 26 26 42 21 275
"ATMG01380" 11 20 25 28 40 16
"ATMG01390" 4524 1728 1696 2174 2737 10435
"ATMG01400" 7 13 11 10 9 15
"ATMG01410" 45 41 37 52 46 31


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