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- > tr
- An object of class "DGELRT"
- $coefficients
- groupLD.0 groupLD.12 groupLD.24 groupLD.36 groupLD.48
- TRINITY_DN4656_c0_g1_i1 -11.663326 -11.003130 -11.439181 -11.010954 -11.669459
- TRINITY_DN2201_c0_g1_i1 -12.656558 -13.428807 -13.531602 -12.509400 -13.046445
- TRINITY_DN14130_c0_g1_i1 -9.956345 -9.891205 -9.444769 -9.004883 -9.263105
- TRINITY_DN11412_c0_g1_i1 -11.717221 -11.365336 -11.534243 -10.931035 -11.414229
- TRINITY_DN3581_c0_g1_i5 -10.528443 -10.314920 -10.232230 -9.666242 -10.356563
- groupLL.0 groupLL.12 groupLL.24 groupLL.36 groupLL.48
- TRINITY_DN4656_c0_g1_i1 -13.07580 -10.421003 -17.44031 -11.088339 -11.98861
- TRINITY_DN2201_c0_g1_i1 -17.44031 -17.440307 -17.44031 -17.440307 -12.60398
- TRINITY_DN14130_c0_g1_i1 -10.13043 -9.556846 -10.85245 -9.821844 -11.35014
- TRINITY_DN11412_c0_g1_i1 -10.23283 -11.728147 -11.98452 -11.505171 -12.01448
- TRINITY_DN3581_c0_g1_i5 -17.44031 -10.627437 -17.44031 -11.315111 -17.44031
- 27255 more rows ...
- $fitted.values
- DRR057059_1.fastq.trim DRR057059_1.fastq.trim2
- TRINITY_DN4656_c0_g1_i1 19.00 19.00
- TRINITY_DN2201_c0_g1_i1 7.00 7.00
- TRINITY_DN14130_c0_g1_i1 105.00 105.00
- TRINITY_DN11412_c0_g1_i1 18.00 18.00
- TRINITY_DN3581_c0_g1_i5 59.23 59.23
- DRR057065_1.fastq.trim DRR057065_1.fastq.trim2
- TRINITY_DN4656_c0_g1_i1 46.00 46.00
- TRINITY_DN2201_c0_g1_i1 4.00 4.00
- TRINITY_DN14130_c0_g1_i1 140.00 140.00
- TRINITY_DN11412_c0_g1_i1 32.00 32.00
- TRINITY_DN3581_c0_g1_i5 91.62 91.62
- DRR057071_1.fastq.trim DRR057071_1.fastq.trim2
- TRINITY_DN4656_c0_g1_i1 33.00 33.00
- TRINITY_DN2201_c0_g1_i1 4.00 4.00
- TRINITY_DN14130_c0_g1_i1 243.00 243.00
- TRINITY_DN11412_c0_g1_i1 30.00 30.00
- TRINITY_DN3581_c0_g1_i5 110.52 110.52
- DRR057077_1.fastq.trim DRR057077_1.fastq.trim2
- TRINITY_DN4656_c0_g1_i1 36.0 36.0
- TRINITY_DN2201_c0_g1_i1 8.0 8.0
- TRINITY_DN14130_c0_g1_i1 268.0 268.0
- TRINITY_DN11412_c0_g1_i1 39.0 39.0
- TRINITY_DN3581_c0_g1_i5 138.3 138.3
- DRR057083_1.fastq.trim DRR057083_1.fastq.trim2
- TRINITY_DN4656_c0_g1_i1 24.00 24.00
- TRINITY_DN2201_c0_g1_i1 6.00 6.00
- TRINITY_DN14130_c0_g1_i1 267.00 267.00
- TRINITY_DN11412_c0_g1_i1 31.00 31.00
- TRINITY_DN3581_c0_g1_i5 89.41 89.41
- DRR057309_1.fastq.trim DRR057309_1.fastq2.trim
- TRINITY_DN4656_c0_g1_i1 8 8
- TRINITY_DN2201_c0_g1_i1 0 0
- TRINITY_DN14130_c0_g1_i1 154 154
- TRINITY_DN11412_c0_g1_i1 139 139
- TRINITY_DN3581_c0_g1_i5 0 0
- DRR057315_1.fastq.trim DRR057315_1.fastq2.trim
- TRINITY_DN4656_c0_g1_i1 163.00 163.00
- TRINITY_DN2201_c0_g1_i1 0.00 0.00
- TRINITY_DN14130_c0_g1_i1 387.00 387.00
- TRINITY_DN11412_c0_g1_i1 44.00 44.00
- TRINITY_DN3581_c0_g1_i5 132.57 132.57
- DRR057321_1.fastq.trim DRR057321_1.fastq2.trim
- TRINITY_DN4656_c0_g1_i1 0 0
- TRINITY_DN2201_c0_g1_i1 0 0
- TRINITY_DN14130_c0_g1_i1 196 196
- TRINITY_DN11412_c0_g1_i1 63 63
- TRINITY_DN3581_c0_g1_i5 0 0
- DRR057327_1.fastq.trim DRR057327_1.fastq2.trim
- TRINITY_DN4656_c0_g1_i1 123 123
- TRINITY_DN2201_c0_g1_i1 0 0
- TRINITY_DN14130_c0_g1_i1 437 437
- TRINITY_DN11412_c0_g1_i1 81 81
- TRINITY_DN3581_c0_g1_i5 98 98
- DRR057333_1.fastq.trim DRR057333_1.fastq2.trim
- TRINITY_DN4656_c0_g1_i1 39 39
- TRINITY_DN2201_c0_g1_i1 21 21
- TRINITY_DN14130_c0_g1_i1 74 74
- TRINITY_DN11412_c0_g1_i1 38 38
- TRINITY_DN3581_c0_g1_i5 0 0
- 27255 more rows ...
- $deviance
- TRINITY_DN4656_c0_g1_i1 TRINITY_DN2201_c0_g1_i1 TRINITY_DN14130_c0_g1_i1
- -1.021405e-14 -4.884981e-15 7.904788e-14
- TRINITY_DN11412_c0_g1_i1 TRINITY_DN3581_c0_g1_i5
- -1.687539e-14 2.844835e-14
- 27255 more elements ...
- $method
- [1] "oneway"
- $unshrunk.coefficients
- groupLD.0 groupLD.12 groupLD.24 groupLD.36 groupLD.48
- TRINITY_DN4656_c0_g1_i1 -11.666429 -11.004732 -11.441659 -11.012569 -11.672581
- TRINITY_DN2201_c0_g1_i1 -12.664958 -13.447079 -13.551873 -12.516646 -13.058875
- TRINITY_DN14130_c0_g1_i1 -9.956907 -9.891731 -9.445106 -9.005100 -9.263386
- TRINITY_DN11412_c0_g1_i1 -11.720496 -11.367638 -11.536970 -10.932526 -11.416647
- TRINITY_DN3581_c0_g1_i5 -10.529439 -10.315724 -10.232971 -9.666662 -10.357402
- groupLL.0 groupLL.12 groupLL.24
- TRINITY_DN4656_c0_g1_i1 -1.308861e+01 -1.042190e+01 -1.000000e+08
- TRINITY_DN2201_c0_g1_i1 -1.000000e+08 -1.000000e+08 -1.000000e+08
- TRINITY_DN14130_c0_g1_i1 -1.013109e+01 -9.557223e+00 -1.085382e+01
- TRINITY_DN11412_c0_g1_i1 -1.023357e+01 -1.173146e+01 -1.198880e+01
- TRINITY_DN3581_c0_g1_i5 -1.000000e+08 -1.062854e+01 -1.000000e+08
- groupLL.36 groupLL.48
- TRINITY_DN4656_c0_g1_i1 -1.109008e+01 -1.199291e+01
- TRINITY_DN2201_c0_g1_i1 -1.000000e+08 -1.261195e+01
- TRINITY_DN14130_c0_g1_i1 -9.822335e+00 -1.135241e+01
- TRINITY_DN11412_c0_g1_i1 -1.150782e+01 -1.201889e+01
- TRINITY_DN3581_c0_g1_i5 -1.131730e+01 -1.000000e+08
- 27255 more rows ...
- $df.residual
- [1] 10 10 10 10 10
- 27255 more elements ...
- $design
- groupLD.0 groupLD.12 groupLD.24 groupLD.36 groupLD.48 groupLL.0 groupLL.12
- 1 1 0 0 0 0 0 0
- 2 1 0 0 0 0 0 0
- 3 0 1 0 0 0 0 0
- 4 0 1 0 0 0 0 0
- 5 0 0 1 0 0 0 0
- groupLL.24 groupLL.36 groupLL.48
- 1 0 0 0
- 2 0 0 0
- 3 0 0 0
- 4 0 0 0
- 5 0 0 0
- 15 more rows ...
- $offset
- [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
- [1,] 14.61087 14.61087 14.83337 14.83337 14.93817 14.93817 14.59609 14.59609
- [,9] [,10] [,11] [,12] [,13] [,14] [,15] [,16]
- [1,] 14.85063 14.85063 15.16805 15.16805 15.51565 15.51565 16.13194 16.13194
- [,17] [,18] [,19] [,20]
- [1,] 15.90227 15.90227 15.65647 15.65647
- attr(,"class")
- [1] "CompressedMatrix"
- attr(,"Dims")
- [1] 5 20
- attr(,"repeat.row")
- [1] TRUE
- attr(,"repeat.col")
- [1] FALSE
- 27255 more rows ...
- $dispersion
- [1] 9.765625e-05 9.765625e-05 9.765625e-05 9.765625e-05 9.765625e-05
- 27255 more elements ...
- $prior.count
- [1] 0.125
- $AveLogCPM
- [1] 3.4470497 0.5781795 5.6177038 3.5133336 3.9841033
- 27255 more elements ...
- $df.residual.zeros
- [1] 9 6 10 10 7
- 27255 more elements ...
- $df.prior
- TRINITY_DN4656_c0_g1_i1 TRINITY_DN2201_c0_g1_i1 TRINITY_DN14130_c0_g1_i1
- 0.3301003 0.3301003 0.1735149
- TRINITY_DN11412_c0_g1_i1 TRINITY_DN3581_c0_g1_i5
- 0.3301003 0.1735149
- 27255 more elements ...
- $var.post
- TRINITY_DN4656_c0_g1_i1 TRINITY_DN2201_c0_g1_i1 TRINITY_DN14130_c0_g1_i1
- 9.162642e-23 2.826892e-22 7.769969e-15
- TRINITY_DN11412_c0_g1_i1 TRINITY_DN3581_c0_g1_i5
- 9.921898e-23 3.965749e-15
- 27255 more elements ...
- $var.prior
- [1] 2.589769e-21 5.420931e-21 1.071458e-19 3.104941e-21 1.122194e-20
- 27255 more elements ...
- $samples
- group lib.size norm.factors
- DRR057059_1.fastq.trim LD.0 2678567 0.8270212
- DRR057059_1.fastq.trim2 LD.0 2678567 0.8270212
- DRR057065_1.fastq.trim LD.12 3416428 0.8099908
- DRR057065_1.fastq.trim2 LD.12 3416428 0.8099908
- DRR057071_1.fastq.trim LD.24 3968907 0.7742702
- 15 more rows ...
- $genes
- Length
- 1 695
- 2 456
- 3 411
- 5 611
- 6 397
- 31180 more rows ...
- $lfc
- [1] 0.5849625
- $table
- logFC unshrunk.logFC logCPM PValue
- TRINITY_DN4656_c0_g1_i1 -0.4604440 -4.621410e-01 3.4470497 1.000000e+00
- TRINITY_DN2201_c0_g1_i1 0.6383368 6.447742e-01 0.5781795 2.434659e-01
- TRINITY_DN14130_c0_g1_i1 -3.0109573 -3.013823e+00 5.6177038 6.931644e-82
- TRINITY_DN11412_c0_g1_i1 -0.8659739 -8.688495e-01 3.5133336 4.170745e-02
- TRINITY_DN3581_c0_g1_i5 -10.2196824 -1.442695e+08 3.9841033 3.479603e-59
- 27255 more rows ...
- $comparison
- [1] "-1*groupLD.48 1*groupLL.48"
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