This web page was produced as an assignment for a course on Statistical Analysis on Microarray Data at Pomona College (return to index)

In this section I discuss running Significance Analysis of Microarrays (SAM) on the microarray data for this project.

From this section and on, I have combined spots into single miRNA by taking the average of the M value for the two spots that go together (if both spots are good, or just the good spot if one spot is bad, or NA if both spots are bad).

Because there was both tumor tissue and normal tissue used in the study, the first SAM that I ran was comparing the miRNA of the tumor and normal tissue.

SAM is testing the hypothesis for each miRNA (i.e. 768 times hypothesis tests since there are 768 distinct miRNA per array)

H0: the miRNA is not able to discriminate between tumor tissue and normal tissue

Ha0: the miRNA is able to discriminate between tumor tissue and normal tissue

With a False Discovery Rate (FDR) set at 0.05, there were 73 miRNA that were found to be significant. In other words, when we set the expect to see about 1 in 20 falsely reported significant genes in the whole experiment, then there were 73 miRNA for which a t-test rejected the null hypothesis.

> summary(norm.sam.tumor,1.3)

SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances

s0 = 0

Number of permutations: 100

MEAN number of falsely called variables is computed.

Delta: 1.3

cutlow: -2.991

cutup: 3.259

p0: 0.748

Identified Genes: 73

Falsely Called Genes: 4.86

FDR: 0.0498

Identified Genes (using Delta = 1.3):

Row d.value stdev rawp q.value R.fold Name

1 429 -7.49 0.0802 0 0 0.6676

2 50 -6.29 0.1798 1.30e-05 0.00187 0.4682 hsa_miR_431

3 553 -6.08 0.1005 1.30e-05 0.00187 0.6522 CONTROL_2

4 124 -5.96 0.2319 1.30e-05 0.00187 0.3823 CONTROL_1

5 129 5.60 0.3399 6.51e-05 0.00686 3.4471 hsa_miR_135b

6 394 -5.19 0.2599 0.000117 0.00686 0.4204 hsa_miR_513

7 317 -5.13 0.2517 0.000117 0.00686 0.4210

8 688 -5.11 0.7208 0.000117 0.00686 0.0972 hsa_miR_196a

9 167 -5.08 0.1655 0.000117 0.00686 0.5558 ambi_miR_2537

10 70 -5.04 0.3538 0.000130 0.00686 0.3037

11 724 -5.00 0.1645 0.000143 0.00686 0.6032

12 263 -5.00 0.0793 0.000143 0.00686 0.7661

13 567 4.84 0.5783 0.000169 0.00695 11.5361 hsa_miR_151

14 221 4.81 0.4253 0.000169 0.00695 4.1530 hsa_miR_214

15 664 -4.52 0.0588 0.000365 0.01171 0.8352 ambi_miR_7081

16 759 4.44 0.7369 0.000391 0.01171 8.4939 hsa_miR_126

17 314 4.42 0.2185 0.000391 0.01171 2.0808 hsa_miR_150

18 602 4.40 0.1699 0.000404 0.01171 1.9313

19 703 -4.39 0.1984 0.000404 0.01171 0.6587

20 583 4.37 0.1156 0.000443 0.01171 1.4630 hsa_miR_143

21 530 4.32 0.2654 0.000456 0.01171 2.0899 CONTROL_8

22 82 4.30 0.1891 0.000456 0.01171 1.8157 CONTROL_1

23 45 -4.28 0.1874 0.000469 0.01171 0.6019

24 643 4.19 0.1087 0.000651 0.01372 1.3868 ambi_miR_4482

25 43 -4.17 0.2719 0.000651 0.01372 0.5757

26 141 -4.17 0.1551 0.000651 0.01372 0.6311 ambi_miR_10594

27 667 -4.16 1.0041 0.000651 0.01372 0.0651 ambi_miR_4482

28 26 -4.10 0.2103 0.000703 0.01372 0.5976 hsa_miR_125b

29 247 4.08 0.1909 0.000703 0.01372 1.6710 hsa_miR_130a

30 680 4.04 0.1223 0.000716 0.01372 1.4122 hsa_miR_329

31 509 4.01 0.6301 0.000755 0.01400 3.1442 hsa_miR_22

32 380 -4.00 0.2463 0.000794 0.01426 0.5555 ambi_miR_10202

33 6 3.94 0.3079 0.000872 0.01519 3.2538 hsa_miR_181b

34 415 3.86 0.1400 0.001133 0.01915 1.4606 hsa_miR_302c_AS

35 570 3.78 1.4356 0.001380 0.02266 3.8711 hsa_miR_345

36 259 -3.72 0.9339 0.001628 0.02598 0.0590 ambi_miR_11576

37 218 3.68 0.2444 0.001745 0.02658 1.8184 hsa_miR_181c

38 4 3.67 0.1303 0.001758 0.02658 1.4380

39 88 -3.65 0.2594 0.001888 0.02668 0.5196 hsa_miR_365

40 375 -3.64 0.3411 0.001914 0.02668 0.5682 hsa_miR_141

41 318 -3.64 0.5404 0.001927 0.02668 0.2563 hsa_miR_511

42 206 3.63 0.1848 0.002044 0.02668 1.9137

43 702 -3.62 0.5295 0.002083 0.02668 0.2248 hsa_miR_346

44 644 3.61 0.1150 0.002135 0.02668 1.3464 ambi_miR_12180

45 515 -3.61 0.2264 0.002135 0.02668 0.5403

46 320 3.61 0.2805 0.002135 0.02668 2.6407 hsa_miR_299_3p

47 416 3.57 0.1961 0.002357 0.02825 1.7136 hsa_miR_199b

48 316 -3.56 0.1843 0.002370 0.02825 0.6219 hsa_miR_18a_AS

49 32 -3.54 0.2444 0.002409 0.02825 0.6840 hsa_miR_486

50 587 -3.54 0.4721 0.002526 0.02903 0.3323

51 123 3.52 0.1632 0.002669 0.03008 1.4475 hsa_let_7a

52 555 3.50 0.6640 0.002826 0.03123 3.3120 CONTROL_27

53 646 -3.48 0.1084 0.002969 0.03215 0.7856

54 289 3.47 0.3999 0.003021 0.03215 2.5268 hsa_miR_335

55 654 -3.36 0.6197 0.003828 0.04000 0.2992 hsa_miR_424

56 147 3.33 0.1170 0.004063 0.04062 1.3295 CONTROL_23

57 199 3.32 0.1121 0.004154 0.04062 1.3162 hsa_miR_519c

58 502 -3.31 0.2809 0.004284 0.04062 0.5542 ambi_miR_2825

59 121 -3.31 0.6430 0.004284 0.04062 0.2520

60 489 -3.30 1.2215 0.004297 0.04062 0.0507

61 35 -3.29 0.3712 0.004375 0.04062 0.5171 hsa_miR_34b

62 581 3.29 0.1322 0.004388 0.04062 1.3492 hsa_miR_383

63 674 -3.28 0.1752 0.004453 0.04062 0.6944 hsa_miR_412

64 310 3.26 0.1570 0.004661 0.04186 1.6397

65 656 -3.22 0.0578 0.005065 0.04444 0.8813 hsa_miR_210

66 562 -3.21 0.3542 0.005104 0.04444 0.4645 hsa_miR_30a_3p

67 241 -3.07 0.4398 0.006680 0.05729 0.4082 hsa_miR_222

68 706 -3.05 0.4624 0.006901 0.05748 0.3804

69 540 -3.05 0.4133 0.007031 0.05772 0.6832 hsa_miR_103

70 162 -3.03 0.2049 0.007370 0.05936 0.6998 hsa_miR_149

71 383 -3.02 0.0910 0.007448 0.05936 0.8346 ambi_miR_3121

72 113 -3.01 0.4564 0.007552 0.05936 0.3554

73 295 -2.99 1.2154 0.007930 0.05996 0.0929

In this SAM, each miRNA is testing

H0: All the tissue types are the same

Ha: The tissue types are not all the same

With a FDR of 0.05, there were 203 miRNA identified as significant.

> summary(norm.sam.all,2.01)

SAM Analysis for the Multi-Class Case with 7 Classes

s0 = 0

Number of permutations: 100

MEAN number of falsely called variables is computed.

Delta: 2.01

cutlow: -Inf

cutup: 3.408

p0: 0.646

Identified Genes: 203

Falsely Called Genes: 15.71

FDR: 0.05

Identified Genes (using Delta = 2.01):

Row d.value stdev rawp q.value R.fold Name

1 570 90.62 0.4510 1.30e-05 0.00323 NA hsa_miR_345

2 509 59.98 0.1392 1.30e-05 0.00323 NA hsa_miR_22

3 561 49.65 0.6024 2.60e-05 0.00430 NA

4 185 33.31 1.2372 5.21e-05 0.00549 NA hsa_miR_202

5 27 29.26 0.8496 7.81e-05 0.00549 NA hsa_miR_337

6 259 26.54 0.7181 7.81e-05 0.00549 NA ambi_miR_11576

7 489 26.12 1.3981 9.11e-05 0.00549 NA

8 295 24.78 1.5405 0.000104 0.00549 NA

9 699 22.21 1.8141 0.000143 0.00549 NA

10 101 20.81 0.7893 0.000182 0.00549 NA hsa_miR_380_5p

11 755 20.75 1.4384 0.000182 0.00549 NA

12 605 18.87 0.0402 0.000208 0.00549 NA hsa_miR_383

13 8 17.74 0.4164 0.000234 0.00549 NA hsa_miR_486

14 452 17.39 0.4578 0.000247 0.00549 NA ambi_miR_10766

15 728 15.99 0.3031 0.000286 0.00549 NA

16 555 15.70 0.5351 0.000286 0.00549 NA CONTROL_27

17 688 15.42 1.3906 0.000286 0.00549 NA hsa_miR_196a

18 359 15.22 1.0307 0.000286 0.00549 NA ambi_miR_3121

19 281 15.14 0.5524 0.000299 0.00549 NA ambi_miR_13237

20 377 14.78 1.0609 0.000299 0.00549 NA hsa_miR_133b

21 123 14.74 0.0282 0.000299 0.00549 NA hsa_let_7a

22 678 13.83 1.4517 0.000352 0.00549 NA hsa_miR_346

23 609 13.73 0.6230 0.000352 0.00549 NA hsa_let_7d

24 667 13.54 2.0535 0.000365 0.00549 NA ambi_miR_4482

25 298 12.68 0.6557 0.000378 0.00549 NA

26 467 12.53 0.0770 0.000391 0.00549 NA hsa_miR_326

27 121 12.04 0.8750 0.000404 0.00549 NA

28 536 11.83 0.5268 0.000404 0.00549 NA hsa_miR_503

29 141 11.80 0.0496 0.000404 0.00549 NA ambi_miR_10594

30 665 11.74 0.9858 0.000404 0.00549 NA ambi_miR_13090

31 474 11.57 2.1651 0.000404 0.00549 NA ambi_miR_13266

32 701 11.49 0.3756 0.000404 0.00549 NA hsa_miR_523

33 187 10.98 0.4445 0.000417 0.00549 NA ambi_miR_7075

34 337 10.80 1.5958 0.000430 0.00549 NA CONTROL_30

35 602 10.63 0.2003 0.000430 0.00549 NA

36 379 10.57 0.3257 0.000430 0.00549 NA ambi_miR_3998

37 515 10.52 0.0846 0.000430 0.00549 NA

38 255 10.38 1.0417 0.000443 0.00549 NA

39 734 10.27 1.3090 0.000443 0.00549 NA hsa_miR_485_5p

40 719 10.20 0.1140 0.000443 0.00549 NA

41 528 10.03 0.1256 0.000456 0.00551 NA ambi_miR_9534

42 198 9.81 0.9123 0.000469 0.00553 NA hsa_miR_522

43 694 9.67 0.0838 0.000495 0.00558 NA

44 61 9.54 0.1297 0.000495 0.00558 NA

45 214 9.54 0.6210 0.000508 0.00559 NA

46 274 9.02 0.1499 0.000573 0.00580 NA

47 207 9.00 0.1860 0.000573 0.00580 NA hsa_miR_340

48 158 8.92 0.3045 0.000573 0.00580 NA hsa_miR_134

49 247 8.87 0.0924 0.000573 0.00580 NA hsa_miR_130a

50 35 8.71 0.5420 0.000586 0.00581 NA hsa_miR_34b

51 162 8.64 0.1714 0.000612 0.00595 NA hsa_miR_149

52 241 8.38 0.5268 0.000677 0.00633 NA hsa_miR_222

53 387 8.37 0.4565 0.000677 0.00633 NA hsa_miR_9_AS

54 65 8.15 0.2991 0.000729 0.00669 NA ambi_miR_7084

55 306 7.96 1.5294 0.000820 0.00739 NA hsa_miR_410

56 129 7.78 0.4497 0.000885 0.00744 NA hsa_miR_135b

57 553 7.77 0.0482 0.000885 0.00744 NA CONTROL_2

58 223 7.76 0.0862 0.000885 0.00744 NA hsa_miR_519c

59 106 7.73 0.4998 0.000898 0.00744 NA

60 522 7.72 0.2124 0.000911 0.00744 NA

61 370 7.61 1.1009 0.000951 0.00744 NA hsa_miR_128a

62 676 7.50 0.1863 0.000990 0.00744 NA hsa_miR_518f_AS

63 586 7.47 0.3822 0.001003 0.00744 NA

64 626 7.39 0.0585 0.001029 0.00744 NA

65 91 7.37 0.1455 0.001055 0.00744 NA ambi_miR_9630

66 86 7.36 0.1286 0.001055 0.00744 NA

67 560 7.32 0.5223 0.001068 0.00744 NA hsa_miR_503

68 742 7.28 0.4407 0.001081 0.00744 NA ambi_miR_4209

69 643 7.27 0.0555 0.001081 0.00744 NA ambi_miR_4482

70 316 7.24 0.0918 0.001081 0.00744 NA hsa_miR_18a_AS

71 680 7.24 0.0577 0.001081 0.00744 NA hsa_miR_329

72 513 7.18 1.0381 0.001081 0.00744 NA

73 432 7.14 0.7236 0.001120 0.00760 NA

74 291 6.77 1.0119 0.001380 0.00925 NA ambi_miR_13124

75 629 6.64 1.2765 0.001432 0.00934 NA hsa_miR_517a

76 178 6.64 0.5254 0.001432 0.00934 NA hsa_miR_296

77 5 6.50 0.2330 0.001549 0.00957 NA hsa_miR_375

78 624 6.49 0.3552 0.001549 0.00957 NA

79 124 6.48 0.3145 0.001563 0.00957 NA CONTROL_1

80 318 6.44 0.9577 0.001589 0.00957 NA hsa_miR_511

81 125 6.44 0.2093 0.001602 0.00957 NA hsa_miR_380_5p

82 225 6.40 0.1823 0.001602 0.00957 NA hsa_miR_384

83 330 6.39 0.3864 0.001602 0.00957 NA hsa_miR_410

84 245 6.32 0.7378 0.001667 0.00984 NA

85 446 6.28 1.0006 0.001719 0.00991 NA

86 627 6.28 0.8585 0.001719 0.00991 NA hsa_miR_10b

87 762 6.25 0.5156 0.001758 0.01000 NA hsa_miR_155

88 657 6.21 1.4104 0.001810 0.01000 NA hsa_miR_377

89 53 6.20 0.3791 0.001810 0.01000 NA hsa_miR_324_5p

90 642 6.19 0.8817 0.001823 0.01000 NA ambi_miR_13190

91 417 6.18 0.6318 0.001849 0.01000 NA hsa_miR_7

92 705 6.16 0.3942 0.001862 0.01000 NA hsa_miR_186

93 314 6.16 0.2751 0.001875 0.01000 NA hsa_miR_150

94 385 6.11 0.1642 0.001927 0.01016 NA hsa_miR_512_3p

95 588 6.07 0.5137 0.001992 0.01040 NA

96 6 6.02 0.7116 0.002018 0.01042 NA hsa_miR_181b

97 551 5.78 0.3645 0.002357 0.01205 NA ambi_miR_10394

98 724 5.69 0.2075 0.002461 0.01245 NA

99 279 5.67 0.0650 0.002487 0.01245 NA

100 380 5.64 0.3623 0.002526 0.01246 NA ambi_miR_10202

101 360 5.63 0.4384 0.002539 0.01246 NA ambi_miR_10133

102 702 5.62 0.9309 0.002565 0.01247 NA hsa_miR_346

103 4 5.57 0.0767 0.002656 0.01279 NA

104 277 5.43 0.3920 0.002969 0.01415 NA

105 616 5.42 0.3573 0.003021 0.01425 NA ambi_miR_13209

106 50 5.41 0.2707 0.003047 0.01425 NA hsa_miR_431

107 541 5.31 0.5101 0.003216 0.01475 NA hsa_miR_495

108 167 5.31 0.1351 0.003216 0.01475 NA ambi_miR_2537

109 438 5.31 0.3974 0.003242 0.01475 NA

110 248 5.25 0.1061 0.003411 0.01529 NA hsa_miR_425

111 49 5.24 0.0515 0.003424 0.01529 NA hsa_miR_373_AS

112 323 5.22 1.0414 0.003503 0.01550 NA

113 335 5.17 0.0980 0.003620 0.01574 NA

114 601 5.17 0.3991 0.003620 0.01574 NA hsa_miR_132

115 689 5.15 0.1253 0.003698 0.01586 NA hsa_miR_520b

116 608 5.14 0.3164 0.003711 0.01586 NA hsa_miR_525

117 600 5.12 1.0733 0.003776 0.01600 NA

118 317 5.07 0.3894 0.003854 0.01619 NA

119 64 5.00 0.3744 0.004010 0.01671 NA hsa_miR_365

120 765 4.96 0.0514 0.004193 0.01729 NA ambi_miR_7920

121 753 4.96 0.3925 0.004219 0.01729 NA

122 415 4.87 0.0870 0.004583 0.01853 NA hsa_miR_302c_AS

123 23 4.85 0.3127 0.004596 0.01853 NA

124 289 4.82 0.5283 0.004687 0.01874 NA hsa_miR_335

125 698 4.81 0.1875 0.004753 0.01885 NA hsa_miR_412

126 530 4.78 0.2495 0.004857 0.01897 NA CONTROL_8

127 514 4.77 0.6560 0.004909 0.01897 NA

128 168 4.77 0.3726 0.004909 0.01897 NA ambi_miR_5

129 409 4.76 0.4048 0.004935 0.01897 NA hsa_miR_512_3p

130 766 4.75 0.1348 0.005013 0.01897 NA ambi_miR_4209

131 56 4.74 0.8029 0.005052 0.01897 NA hsa_miR_26a

132 256 4.74 0.1959 0.005052 0.01897 NA ambi_miR_7103

133 633 4.72 0.3981 0.005130 0.01912 NA hsa_miR_377

134 113 4.66 0.6786 0.005469 0.02023 NA

135 349 4.63 0.6822 0.005651 0.02075 NA hsa_miR_517c

136 707 4.59 0.3948 0.005820 0.02122 NA

137 628 4.57 0.6183 0.005924 0.02144 NA hsa_miR_505

138 2 4.56 1.3474 0.006029 0.02166 NA hsa_miR_125b

139 145 4.53 1.3327 0.006341 0.02262 NA CONTROL_1

140 218 4.51 0.2094 0.006406 0.02269 NA hsa_miR_181c

141 683 4.49 1.2486 0.006523 0.02294 NA

142 391 4.47 0.7266 0.006641 0.02302 NA hsa_miR_302c_AS

143 437 4.47 0.5881 0.006641 0.02302 NA hsa_miR_148a

144 28 4.45 0.0714 0.006732 0.02308 NA

145 512 4.44 0.2384 0.006771 0.02308 NA

146 429 4.43 0.0812 0.006797 0.02308 NA

147 132 4.39 0.3414 0.006979 0.02347 NA

148 130 4.38 0.7052 0.007005 0.02347 NA

149 764 4.37 0.5077 0.007083 0.02357 NA ambi_miR_8488

150 315 4.35 2.4541 0.007188 0.02376 NA ambi_miR_13124

151 527 4.31 0.1370 0.007461 0.02450 NA ambi_miR_5074

152 414 4.30 2.4187 0.007539 0.02459 NA hsa_miR_221

153 579 4.29 0.4936 0.007708 0.02498 NA hsa_miR_100

154 411 4.27 0.6346 0.007878 0.02532 NA hsa_miR_9_AS

155 394 4.26 0.6050 0.007917 0.02532 NA hsa_miR_513

156 221 4.24 1.0840 0.008073 0.02566 NA hsa_miR_214

157 640 4.20 1.4436 0.008490 0.02681 NA ambi_miR_7081

158 144 4.17 0.2970 0.008737 0.02741 NA ambi_miR_11143

159 591 4.16 1.0474 0.008867 0.02748 NA

160 687 4.16 0.6025 0.008867 0.02748 NA hsa_miR_302a

161 559 4.14 0.1873 0.009115 0.02805 NA hsa_miR_520e

162 271 4.14 0.2330 0.009167 0.02805 NA hsa_miR_130a

163 71 4.10 0.1119 0.009583 0.02915 NA hsa_miR_544

164 476 4.09 0.3177 0.009661 0.02921 NA ambi_miR_10766

165 52 4.08 2.3412 0.009844 0.02926 NA hsa_miR_381

166 523 4.08 0.0852 0.009844 0.02926 NA ambi_miR_7510

167 448 4.07 1.4428 0.009883 0.02926 NA

168 690 4.06 0.4057 0.009974 0.02926 NA hsa_miR_498

169 267 4.06 0.2152 0.009974 0.02926 NA

170 94 4.02 2.1153 0.010391 0.03028 NA

171 24 4.02 1.6504 0.010443 0.03028 NA

172 580 3.97 0.1421 0.011198 0.03228 NA

173 735 3.95 0.3007 0.011289 0.03235 NA hsa_miR_126

174 339 3.92 1.2604 0.011758 0.03350 NA CONTROL_48

175 55 3.88 2.0547 0.012122 0.03434 NA

176 16 3.85 2.1992 0.012591 0.03538 NA CONTROL_1

177 236 3.84 0.0221 0.012630 0.03538 NA

178 492 3.82 1.8648 0.013034 0.03630 NA

179 587 3.81 1.3354 0.013346 0.03696 NA

180 66 3.79 1.4291 0.013490 0.03715 NA ambi_miR_7055

181 82 3.78 0.2230 0.013750 0.03766 NA CONTROL_1

182 73 3.77 2.2194 0.013932 0.03792 NA hsa_miR_373_AS

183 745 3.76 0.1290 0.013997 0.03792 NA CONTROL_31

184 544 3.74 0.2357 0.014375 0.03873 NA hsa_miR_224

185 257 3.68 1.5474 0.015208 0.04068 NA ambi_miR_13237

186 34 3.68 2.3934 0.015260 0.04068 NA hsa_miR_330

187 181 3.65 0.2490 0.015781 0.04184 NA hsa_miR_516_5p

188 353 3.63 0.7662 0.016120 0.04251 NA hsa_miR_133b

189 46 3.59 0.1574 0.016771 0.04399 NA

190 371 3.58 0.7029 0.016940 0.04420 NA hsa_miR_19a

191 706 3.55 1.3220 0.017565 0.04536 NA

192 328 3.54 0.1856 0.017565 0.04536 NA hsa_miR_496

193 249 3.49 0.5027 0.018464 0.04725 NA

194 590 3.49 0.1256 0.018490 0.04725 NA hsa_miR_30b

195 647 3.48 0.2040 0.018828 0.04763 NA hsa_miR_539

196 13 3.47 2.4226 0.018984 0.04763 NA CONTROL_1

197 70 3.47 1.0676 0.018984 0.04763 NA

198 216 3.47 0.0618 0.019023 0.04763 NA

199 542 3.46 0.4283 0.019232 0.04780 NA hsa_miR_182_AS

200 743 3.45 0.6468 0.019284 0.04780 NA ambi_miR_7912

201 226 3.43 0.2089 0.019831 0.04870 NA hsa_miR_31

202 169 3.43 0.6770 0.019844 0.04870 NA CONTROL_1

203 32 3.41 0.4598 0.020456 0.04996 NA hsa_miR_486

The miRNA lists for this part (SAM) of the project are not the same as for the previous part (significant genes). This suggests that the miRNA that distinguish between ARMS and ERMS or between PRMS and GIST are not the same miRNA that can be used to distinguish between tumor and normal tissue and they are not the same as those miRNA that are the most significant in distinguishing that the 7 types of tissue that have at least 2 samples are not all the same tissue type.

The differences in the methods used in this section and the previous section are that in limma is a linear analysis of microarray data using information from the entire experiment to help estimate standard errors. SAM uses the microarray data permuting the names of the arrays to simulate what a null distribution of data might look like under the same experimental conditions as the microarrays were put under in the real comparison.

I trust the SAM method more than limma for my data, because as we saw in the section on interesting problems with data, there are some very bad arrays (such as ones that do not have any red on them, or others that are completely red on the background too) that I am not confident that normalization will fix entirely. By permuting the names of the arrays that seems as though it would provide a better idea of which miRNA are significant relative to the rest of the data than when using limma which uses a standard error from all the microarray data together.

I think it is safer to trust cutoffs in which there are fewer comparison groups. The normal versus tumor test is easier to trust the cutoffs because the miRNA are just testing the comparison between those two groups. When comparing all of the types of tissue, a miRNA might be really significant if it just distinguishes between two types of tissue really well because in this multiple comparison test, we are only testing if they are all the same versus the tissue types are not all the same.

To me it makes the most sense to trust the FDR (as opposed to FWER or just the significance level) because then it seems like you have more control over how many miRNA you find as significant when they are not supposed to be.

This website was designed by Austen Head.

Email: austen [dot] head [at] pomona [dot] edu

Pomona Math Department