Relative log expression
Source:R/AllGenerics.R, R/relativeLogExpression-methods.R
relativeLogExpression.RdRelative log expression
Usage
relativeLogExpression(object, ...)
# S4 method for matrix
relativeLogExpression(object)
# S4 method for SummarizedExperiment
relativeLogExpression(object)Examples
## bcbioRNASeq ====
data(bcb)
relativeLogExpression(bcb)
#> → Applying relative log expression (RLE) normalization.
#> control_rep1 control_rep2 control_rep3 fa_day7_rep1
#> ENSMUSG00000000001 29079.46987 3.993762e+04 28051.06900 33200.51560
#> ENSMUSG00000000003 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000028 292.10568 6.676320e+01 0.00000 140.44116
#> ENSMUSG00000000049 1724.64074 8.581166e+02 971.01990 1019.88219
#> ENSMUSG00000000058 27390.90820 1.461607e+04 28665.43201 26843.59188
#> ENSMUSG00000000078 10608.57122 1.130126e+04 10178.98992 93406.48664
#> ENSMUSG00000000085 3940.63288 3.733105e+03 0.00000 0.00000
#> ENSMUSG00000000088 114444.25711 8.269729e+04 97112.68634 42656.04100
#> ENSMUSG00000000093 4051.91675 5.266739e+03 4788.48240 4643.68935
#> ENSMUSG00000000094 248.68272 2.357380e+02 124.78236 209.29084
#> ENSMUSG00000000120 152.76330 1.221911e+02 139.24572 2050.88562
#> ENSMUSG00000000125 0.00000 0.000000e+00 0.00000 30.48569
#> ENSMUSG00000000126 158.05588 1.912080e+02 58.01735 150.46858
#> ENSMUSG00000000127 2489.23486 1.418223e+03 1381.80293 1344.53984
#> ENSMUSG00000000149 25182.90497 2.703181e+04 25107.04666 58859.00348
#> ENSMUSG00000000157 0.00000 0.000000e+00 135.22001 988.36437
#> ENSMUSG00000000159 2657.63724 0.000000e+00 2622.52864 1984.36135
#> ENSMUSG00000000167 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000171 73252.71370 5.359653e+04 77518.15556 30968.45847
#> ENSMUSG00000000182 0.00000 4.329954e+01 186.40959 159.82890
#> ENSMUSG00000000183 188.14626 0.000000e+00 61.02399 286.71961
#> ENSMUSG00000000184 7191.27552 3.885354e+03 2853.07113 5471.02234
#> ENSMUSG00000000197 852.96466 2.140540e+02 590.08123 0.00000
#> ENSMUSG00000000202 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000204 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000214 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000215 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000216 19003.75029 1.553600e+04 17566.69909 20144.11096
#> ENSMUSG00000000223 250.45556 2.116928e+02 0.00000 149.88965
#> ENSMUSG00000000247 115.08304 0.000000e+00 67.88727 124.44131
#> ENSMUSG00000000248 0.00000 0.000000e+00 0.00000 765.18610
#> ENSMUSG00000000253 4932.13708 4.349771e+03 6729.65488 2767.20616
#> ENSMUSG00000000275 0.00000 7.405498e-03 0.00000 0.00000
#> ENSMUSG00000000276 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000278 42237.32010 2.965737e+04 26895.16827 14801.15182
#> ENSMUSG00000000282 7369.59090 9.887735e+03 6142.63369 6078.24254
#> ENSMUSG00000000290 0.00000 0.000000e+00 501.34661 0.00000
#> ENSMUSG00000000295 512.28096 4.705931e+02 661.07948 329.80056
#> ENSMUSG00000000296 989.54295 8.518676e+01 651.48096 113.71922
#> ENSMUSG00000000301 0.00000 0.000000e+00 1525.51705 0.00000
#> ENSMUSG00000000303 39188.42937 5.052585e+04 47581.09216 50229.24815
#> ENSMUSG00000000305 494.81280 1.713476e+02 311.80882 504.97643
#> ENSMUSG00000000308 0.00000 0.000000e+00 390.87094 0.00000
#> ENSMUSG00000000317 1472.42832 9.407288e+02 1254.78272 2455.15679
#> ENSMUSG00000000318 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000320 665.20152 1.673314e+03 2933.17929 1598.63195
#> ENSMUSG00000000326 22989.14671 7.661558e+04 28193.41821 13532.96146
#> ENSMUSG00000000339 5760.61469 4.172154e+03 3604.07386 1871.83122
#> ENSMUSG00000000340 42892.72739 2.926806e+04 42934.87523 15385.62489
#> ENSMUSG00000000346 175913.08416 2.936623e+05 121223.45245 126806.26592
#> ENSMUSG00000000355 2589.95998 4.482318e+03 3583.56614 6175.94622
#> ENSMUSG00000000359 822.77833 3.479518e+02 589.65180 692.98663
#> ENSMUSG00000000374 29674.27460 1.316414e+04 15035.78332 9883.11486
#> ENSMUSG00000000378 990.65841 3.486947e+02 333.03392 0.00000
#> ENSMUSG00000000384 5264.62593 2.536487e+04 5925.98557 2417.22243
#> ENSMUSG00000000385 29047.51283 3.536797e+04 29915.77108 37629.62721
#> ENSMUSG00000000392 37.64085 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000402 7808.83012 1.478123e+04 7737.52983 5879.11575
#> ENSMUSG00000000411 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000420 9005.89364 4.903873e+03 4647.37279 15988.58919
#> ENSMUSG00000000435 61.31414 6.765289e+01 124.94036 58.95392
#> ENSMUSG00000000439 8652.21134 9.552220e+03 8282.87451 9938.48419
#> ENSMUSG00000000440 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000441 7474.69081 9.004951e+03 7097.34520 2165.62756
#> ENSMUSG00000000489 2946.62535 1.168701e+05 3863.40010 15591.51719
#> ENSMUSG00000000530 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000531 1074.75530 1.313853e+03 1384.33882 1367.92330
#> ENSMUSG00000000532 13208.81088 2.483232e+04 13383.12332 10513.02207
#> ENSMUSG00000000560 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000562 425.33266 3.554661e+02 707.01008 930.79320
#> ENSMUSG00000000567 1021.35671 9.349186e+02 1710.24809 15841.07052
#> ENSMUSG00000000581 25457.39356 2.045902e+04 19566.27938 9312.74645
#> ENSMUSG00000000594 123431.37690 1.388797e+05 131758.67666 41745.30371
#> ENSMUSG00000000605 16173.67138 8.873027e+03 10438.12278 9002.48635
#> ENSMUSG00000000617 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000627 182.11800 1.698998e+02 255.24488 183.31170
#> ENSMUSG00000000628 171.94856 2.603896e+02 7448.30221 639.20977
#> ENSMUSG00000000631 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000632 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000000673 30364.64397 2.731805e+04 25466.03340 2942.07868
#> ENSMUSG00000020152 67741.16009 4.838252e+04 73897.89419 47246.57211
#> ENSMUSG00000020333 0.00000 0.000000e+00 61.51732 0.00000
#> ENSMUSG00000020676 0.00000 0.000000e+00 191.72079 120.66924
#> ENSMUSG00000020875 0.00000 3.207954e+03 590.73997 3105.45428
#> ENSMUSG00000026315 3532.88227 3.150330e+03 4845.42420 6868.36492
#> ENSMUSG00000026535 852.26490 2.390487e+02 413.02529 3119.40081
#> ENSMUSG00000028494 2809.65437 1.725326e+03 659.23043 18748.79054
#> ENSMUSG00000029231 5743.69936 0.000000e+00 828.00351 1974.41252
#> ENSMUSG00000029534 0.00000 0.000000e+00 488.26642 0.00000
#> ENSMUSG00000029730 1819.28660 3.589806e+03 2776.76385 1500.88969
#> ENSMUSG00000032050 13584.73258 9.019779e+03 5703.49964 15924.68115
#> ENSMUSG00000035352 0.00000 2.189452e+01 0.00000 585.96232
#> ENSMUSG00000035385 0.00000 2.192792e+01 0.00000 14094.26778
#> ENSMUSG00000038257 0.00000 2.183071e+01 0.00000 0.00000
#> ENSMUSG00000044807 0.00000 0.000000e+00 0.00000 0.00000
#> ENSMUSG00000048583 453.99893 0.000000e+00 0.00000 116.28108
#> ENSMUSG00000055022 0.00000 5.009799e+02 1746.52758 2373.39840
#> ENSMUSG00000061689 0.00000 0.000000e+00 109.39553 0.00000
#> ENSMUSG00000062661 2891.72266 3.136288e+03 3169.15695 7270.64192
#> ENSMUSG00000074340 0.00000 6.698192e+01 326.45718 212.37428
#> fa_day7_rep2 fa_day7_rep3
#> ENSMUSG00000000001 33200.51560 3.592823e+04
#> ENSMUSG00000000003 0.00000 0.000000e+00
#> ENSMUSG00000000028 0.00000 1.535150e+02
#> ENSMUSG00000000049 221.96734 1.153767e+03
#> ENSMUSG00000000058 26121.56868 2.093754e+04
#> ENSMUSG00000000078 53128.23677 6.063816e+04
#> ENSMUSG00000000085 0.00000 1.542110e+03
#> ENSMUSG00000000088 44981.33452 8.148414e+04
#> ENSMUSG00000000093 8522.07416 5.304040e+03
#> ENSMUSG00000000094 295.35992 1.657575e+02
#> ENSMUSG00000000120 4432.93460 1.018416e+03
#> ENSMUSG00000000125 32.10212 0.000000e+00
#> ENSMUSG00000000126 365.61199 0.000000e+00
#> ENSMUSG00000000127 2978.54296 3.032257e+04
#> ENSMUSG00000000149 19660.49583 3.538776e+04
#> ENSMUSG00000000157 1162.02322 2.036566e-01
#> ENSMUSG00000000159 0.00000 0.000000e+00
#> ENSMUSG00000000167 0.00000 2.833703e+02
#> ENSMUSG00000000171 27243.34963 3.507709e+04
#> ENSMUSG00000000182 67.16399 1.289190e+03
#> ENSMUSG00000000183 291.63175 3.378648e+01
#> ENSMUSG00000000184 4046.37628 3.436781e+03
#> ENSMUSG00000000197 0.00000 0.000000e+00
#> ENSMUSG00000000202 0.00000 0.000000e+00
#> ENSMUSG00000000204 182.92447 1.712789e+02
#> ENSMUSG00000000214 0.00000 0.000000e+00
#> ENSMUSG00000000215 0.00000 0.000000e+00
#> ENSMUSG00000000216 15271.19808 2.702576e+04
#> ENSMUSG00000000223 294.40309 3.760806e+02
#> ENSMUSG00000000247 122.47318 6.387494e+01
#> ENSMUSG00000000248 399.91443 0.000000e+00
#> ENSMUSG00000000253 6230.23012 4.137989e+03
#> ENSMUSG00000000275 0.00000 6.963156e+01
#> ENSMUSG00000000276 1258.97530 0.000000e+00
#> ENSMUSG00000000278 25082.92331 1.610980e+04
#> ENSMUSG00000000282 8556.64197 6.120712e+03
#> ENSMUSG00000000290 1417.81680 2.714433e+02
#> ENSMUSG00000000295 393.44898 8.773150e+02
#> ENSMUSG00000000296 363.60560 8.422560e+02
#> ENSMUSG00000000301 91.41795 0.000000e+00
#> ENSMUSG00000000303 40876.35276 5.354249e+04
#> ENSMUSG00000000305 354.70063 3.840746e+02
#> ENSMUSG00000000308 983.29616 1.638874e+03
#> ENSMUSG00000000317 1935.05561 1.936542e+03
#> ENSMUSG00000000318 0.00000 0.000000e+00
#> ENSMUSG00000000320 1664.66376 1.267842e+03
#> ENSMUSG00000000326 54279.25475 2.602356e+04
#> ENSMUSG00000000339 1348.34796 3.346591e+03
#> ENSMUSG00000000340 12381.23070 2.145546e+04
#> ENSMUSG00000000346 158435.22907 1.496809e+05
#> ENSMUSG00000000355 938.55948 9.655250e+02
#> ENSMUSG00000000359 1050.73558 1.910338e+02
#> ENSMUSG00000000374 11143.03214 2.615702e+04
#> ENSMUSG00000000378 343.63504 1.071496e+03
#> ENSMUSG00000000384 5189.74607 4.202567e+03
#> ENSMUSG00000000385 33277.36868 3.164981e+04
#> ENSMUSG00000000392 0.00000 0.000000e+00
#> ENSMUSG00000000402 10303.97441 4.037148e+03
#> ENSMUSG00000000411 64.13759 0.000000e+00
#> ENSMUSG00000000420 9790.67529 5.915651e+03
#> ENSMUSG00000000435 91.73932 2.706315e+02
#> ENSMUSG00000000439 7976.74768 1.062347e+04
#> ENSMUSG00000000440 0.00000 2.746017e+02
#> ENSMUSG00000000441 709.39662 0.000000e+00
#> ENSMUSG00000000489 5474.99501 1.304788e+04
#> ENSMUSG00000000530 0.00000 0.000000e+00
#> ENSMUSG00000000531 2291.08268 8.088236e+02
#> ENSMUSG00000000532 15830.63421 1.408228e+04
#> ENSMUSG00000000560 0.00000 0.000000e+00
#> ENSMUSG00000000562 430.49635 2.540617e+02
#> ENSMUSG00000000567 6872.96154 9.850788e+03
#> ENSMUSG00000000581 8161.67420 1.916208e+04
#> ENSMUSG00000000594 41787.66167 7.715846e+04
#> ENSMUSG00000000605 6344.63586 1.321798e+04
#> ENSMUSG00000000617 0.00000 0.000000e+00
#> ENSMUSG00000000627 194.48526 1.320440e+02
#> ENSMUSG00000000628 443.70756 7.104966e+02
#> ENSMUSG00000000631 0.00000 2.428862e-01
#> ENSMUSG00000000632 0.00000 0.000000e+00
#> ENSMUSG00000000673 6816.16277 6.167128e+03
#> ENSMUSG00000020152 42692.03469 5.936757e+04
#> ENSMUSG00000020333 0.00000 0.000000e+00
#> ENSMUSG00000020676 419.52917 2.485117e+02
#> ENSMUSG00000020875 5205.05031 2.259998e+03
#> ENSMUSG00000026315 5567.85732 3.293441e+03
#> ENSMUSG00000026535 4529.62017 5.738530e+03
#> ENSMUSG00000028494 7428.58279 9.967974e+03
#> ENSMUSG00000029231 8122.17295 9.546387e+02
#> ENSMUSG00000029534 0.00000 0.000000e+00
#> ENSMUSG00000029730 3087.82815 5.628685e+03
#> ENSMUSG00000032050 6988.15702 1.454757e+03
#> ENSMUSG00000035352 452.23614 5.300820e+02
#> ENSMUSG00000035385 11783.42466 2.331916e+04
#> ENSMUSG00000038257 0.00000 0.000000e+00
#> ENSMUSG00000044807 0.00000 0.000000e+00
#> ENSMUSG00000048583 141.47991 0.000000e+00
#> ENSMUSG00000055022 0.00000 7.349491e+02
#> ENSMUSG00000061689 0.00000 0.000000e+00
#> ENSMUSG00000062661 1050.76385 1.588083e+03
#> ENSMUSG00000074340 0.00000 4.949328e+02