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Relative log expression

Usage

relativeLogExpression(object, ...)

# S4 method for matrix
relativeLogExpression(object)

# S4 method for SummarizedExperiment
relativeLogExpression(object)

Arguments

object

Object.

...

Additional arguments.

Value

matrix.

Note

Updated 2020-01-20.

References

Anders and Huber (2010).

Author

Lorena Pantano, Michael Steinbaugh

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