## Warning: multiple methods tables found for 'grep'
## Warning: multiple methods tables found for 'grepl'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'IRanges'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'IRanges'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'AnnotationDbi'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'AnnotationDbi'
## Warning: replacing previous import by 'S4Vectors::grepl' when loading
## 'GenomeInfoDb'
## Warning: replacing previous import by 'S4Vectors::grep' when loading
## 'GenomeInfoDb'
## Version Okay
## (0.00153,0.279] (0.279,0.445] (0.445,0.633] (0.633,0.845]
## 1.207297 1.207297 1.207297 1.207297
## (0.845,1.08] (1.08,1.36] (1.36,1.66] (1.66,2.01]
## 1.207297 1.207297 1.207297 1.207297
## (2.01,2.4] (2.4,2.84] (2.84,3.34] (3.34,3.9]
## 1.207297 1.207297 1.278617 1.294579
## (3.9,4.54] (4.54,5.26] (5.26,6.07] (6.07,6.99]
## 1.420138 1.420138 1.653459 2.730194
## (6.99,10.5]
## 4.296567
In the LPS stimulation, testing for any time effect, when adjusting for ngeneson we detect 1359 differentially expressed genes. When we don’t adjust for ngeneson, we detect 1996 genes.
## [1] "(Intercept)" "cngeneson" "StimPAM" "StimPIC"
## [5] "StimLPS:Time2h" "StimPAM:Time2h" "StimPIC:Time2h" "StimLPS:Time4h"
## [9] "StimPAM:Time4h" "StimPIC:Time4h" "StimLPS:Time6h" "StimPAM:Time6h"
## [13] "StimPIC:Time6h"
## coefficient module P Z cont_P
## 1: StimLPS:Time2h CORE_ANTIVIRAL 2.255322e-28 11.047449 4.702541e-10
## 2: StimLPS:Time2h GO:0000002 3.119439e-02 -2.154584 8.465066e-03
## 3: StimLPS:Time2h GO:0000009 2.448368e-01 -1.162982 5.874596e-01
## 4: StimLPS:Time2h GO:0000026 2.448368e-01 -1.162982 5.874596e-01
## 5: StimLPS:Time2h GO:0000028 2.414226e-01 -1.171438 2.259393e-01
## ---
## 25394: StimPIC:Time6h GO:2001241 2.427907e-04 3.669747 4.015525e-02
## 25395: StimPIC:Time6h GO:2001243 4.023620e-02 2.051316 7.727905e-02
## 25396: StimPIC:Time6h GO:2001244 1.374592e-01 1.485320 4.417704e-03
## 25397: StimPIC:Time6h PEAKED_INFLAM 4.596063e-05 4.075272 3.953161e-03
## 25398: StimPIC:Time6h SUSTAINED_INFLAM 2.714891e-70 17.724464 4.591031e-17
## cont_Z disc_P disc_Z adjp
## 1: 6.8375075 1.855746e-14 8.7859450 3.535844e-26
## 2: -2.6846307 7.177675e-01 -0.3624115 8.505368e-02
## 3: -0.5442115 2.734897e-01 -1.1004936 3.852028e-01
## 4: -0.5442115 2.734897e-01 -1.1004936 3.852028e-01
## 5: -1.2176058 6.615149e-01 -0.4390582 3.831804e-01
## ---
## 25394: 2.0787757 2.395321e-03 3.1110302 4.982239e-03
## 25395: 1.7838120 2.664162e-01 1.1171867 1.854072e-01
## 25396: 2.9088372 4.206981e-01 -0.8082781 3.922243e-01
## 25397: 2.9421606 5.617229e-03 2.8211440 1.179099e-03
## 25398: 9.8331320 1.204056e-30 15.2330452 7.661423e-67
## coefficient GOID P Z
## 1: StimLPS:Time2h CORE_ANTIVIRAL 2.255322e-28 11.047449
## 2: StimLPS:Time4h CORE_ANTIVIRAL 0.000000e+00 44.419672
## 3: StimLPS:Time6h CORE_ANTIVIRAL 0.000000e+00 42.019192
## 4: StimPAM:Time2h CORE_ANTIVIRAL 5.450429e-04 3.457584
## 5: StimPAM:Time4h CORE_ANTIVIRAL 1.693595e-20 9.280075
## ---
## 25394: StimPAM:Time4h SUSTAINED_INFLAM 3.786028e-156 26.621909
## 25395: StimPAM:Time6h SUSTAINED_INFLAM 4.990566e-173 28.042072
## 25396: StimPIC:Time2h SUSTAINED_INFLAM 1.992389e-31 11.662028
## 25397: StimPIC:Time4h SUSTAINED_INFLAM 2.442928e-45 14.131102
## 25398: StimPIC:Time6h SUSTAINED_INFLAM 2.714891e-70 17.724464
## cont_P cont_Z disc_P disc_Z adjp
## 1: 4.702541e-10 6.837508 1.855746e-14 8.7859450 3.535844e-26
## 2: 3.085647e-42 21.975989 2.500349e-73 40.8429134 0.000000e+00
## 3: 3.526389e-44 23.086788 1.069596e-65 36.3373227 0.000000e+00
## 4: 9.787409e-06 4.617583 7.859410e-01 0.2721786 4.841903e-03
## 5: 6.183786e-11 7.173364 3.233500e-08 5.9506434 2.430166e-18
## ---
## 25394: 4.187826e-42 20.481303 1.392422e-33 17.1677623 1.602626e-152
## 25395: 1.190721e-37 18.780511 3.688710e-42 20.8769678 4.225013e-169
## 25396: 2.116803e-09 6.470005 2.433396e-17 10.0225939 1.405630e-28
## 25397: 3.426867e-15 8.952578 1.840406e-19 11.0318174 2.297981e-42
## 25398: 4.591031e-17 9.833132 1.204056e-30 15.2330452 7.661423e-67
## TERM Stim effectfilter include_sub
## 1: CORE_ANTIVIRAL StimLPS TRUE TRUE
## 2: CORE_ANTIVIRAL StimLPS TRUE TRUE
## 3: CORE_ANTIVIRAL StimLPS TRUE TRUE
## 4: CORE_ANTIVIRAL StimPAM FALSE FALSE
## 5: CORE_ANTIVIRAL StimPAM TRUE TRUE
## ---
## 25394: SUSTAINED_INFLAM StimPAM TRUE TRUE
## 25395: SUSTAINED_INFLAM StimPAM TRUE TRUE
## 25396: SUSTAINED_INFLAM StimPIC TRUE TRUE
## 25397: SUSTAINED_INFLAM StimPIC TRUE TRUE
## 25398: SUSTAINED_INFLAM StimPIC TRUE TRUE
## coefficient GOID P Z
## 1: StimLPS:Time2h CORE_ANTIVIRAL 2.255322e-28 11.047449
## 2: StimLPS:Time4h CORE_ANTIVIRAL 0.000000e+00 44.419672
## 3: StimLPS:Time6h CORE_ANTIVIRAL 0.000000e+00 42.019192
## 4: StimPAM:Time2h CORE_ANTIVIRAL 5.450429e-04 3.457584
## 5: StimPAM:Time4h CORE_ANTIVIRAL 1.693595e-20 9.280075
## ---
## 25394: StimPAM:Time4h SUSTAINED_INFLAM 3.786028e-156 26.621909
## 25395: StimPAM:Time6h SUSTAINED_INFLAM 4.990566e-173 28.042072
## 25396: StimPIC:Time2h SUSTAINED_INFLAM 1.992389e-31 11.662028
## 25397: StimPIC:Time4h SUSTAINED_INFLAM 2.442928e-45 14.131102
## 25398: StimPIC:Time6h SUSTAINED_INFLAM 2.714891e-70 17.724464
## cont_P cont_Z disc_P disc_Z adjp
## 1: 4.702541e-10 6.837508 1.855746e-14 8.7859450 3.535844e-26
## 2: 3.085647e-42 21.975989 2.500349e-73 40.8429134 0.000000e+00
## 3: 3.526389e-44 23.086788 1.069596e-65 36.3373227 0.000000e+00
## 4: 9.787409e-06 4.617583 7.859410e-01 0.2721786 4.841903e-03
## 5: 6.183786e-11 7.173364 3.233500e-08 5.9506434 2.430166e-18
## ---
## 25394: 4.187826e-42 20.481303 1.392422e-33 17.1677623 1.602626e-152
## 25395: 1.190721e-37 18.780511 3.688710e-42 20.8769678 4.225013e-169
## 25396: 2.116803e-09 6.470005 2.433396e-17 10.0225939 1.405630e-28
## 25397: 3.426867e-15 8.952578 1.840406e-19 11.0318174 2.297981e-42
## 25398: 4.591031e-17 9.833132 1.204056e-30 15.2330452 7.661423e-67
## TERM Stim effectfilter include_sub include
## 1: CORE_ANTIVIRAL StimLPS TRUE TRUE TRUE
## 2: CORE_ANTIVIRAL StimLPS TRUE TRUE TRUE
## 3: CORE_ANTIVIRAL StimLPS TRUE TRUE TRUE
## 4: CORE_ANTIVIRAL StimPAM FALSE FALSE TRUE
## 5: CORE_ANTIVIRAL StimPAM TRUE TRUE TRUE
## ---
## 25394: SUSTAINED_INFLAM StimPAM TRUE TRUE TRUE
## 25395: SUSTAINED_INFLAM StimPAM TRUE TRUE TRUE
## 25396: SUSTAINED_INFLAM StimPIC TRUE TRUE TRUE
## 25397: SUSTAINED_INFLAM StimPIC TRUE TRUE TRUE
## 25398: SUSTAINED_INFLAM StimPIC TRUE TRUE TRUE
## TERM
## 1: CORE_ANTIVIRAL
## 2: CORE_ANTIVIRAL
## 3: CORE_ANTIVIRAL
## 4: nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
## 5: nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
## ---
## 3671: PEAKED_INFLAM
## 3672: PEAKED_INFLAM
## 3673: SUSTAINED_INFLAM
## 3674: SUSTAINED_INFLAM
## 3675: SUSTAINED_INFLAM
## GOID include coefficient Stim effectfilter
## 1: CORE_ANTIVIRAL TRUE StimLPS:Time2h StimLPS TRUE
## 2: CORE_ANTIVIRAL TRUE StimLPS:Time4h StimLPS TRUE
## 3: CORE_ANTIVIRAL TRUE StimLPS:Time6h StimLPS TRUE
## 4: GO:0000288 TRUE StimLPS:Time2h StimLPS TRUE
## 5: GO:0000288 TRUE StimLPS:Time4h StimLPS TRUE
## ---
## 3671: PEAKED_INFLAM TRUE StimLPS:Time4h StimLPS FALSE
## 3672: PEAKED_INFLAM TRUE StimLPS:Time6h StimLPS FALSE
## 3673: SUSTAINED_INFLAM TRUE StimLPS:Time2h StimLPS TRUE
## 3674: SUSTAINED_INFLAM TRUE StimLPS:Time4h StimLPS TRUE
## 3675: SUSTAINED_INFLAM TRUE StimLPS:Time6h StimLPS TRUE
## variable value component
## 1: P 2.255322e-28 P
## 2: P 0.000000e+00 P
## 3: P 0.000000e+00 P
## 4: P 6.098448e-14 P
## 5: P 7.066308e-15 P
## ---
## 3671: include_sub 0.000000e+00 include
## 3672: include_sub 0.000000e+00 include
## 3673: include_sub 1.000000e+00 include
## 3674: include_sub 1.000000e+00 include
## 3675: include_sub 1.000000e+00 include
## TERM
## 1: CORE_ANTIVIRAL
## 2: CORE_ANTIVIRAL
## 3: CORE_ANTIVIRAL
## 4: nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
## 5: nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay
## ---
## 3671: PEAKED_INFLAM
## 3672: PEAKED_INFLAM
## 3673: SUSTAINED_INFLAM
## 3674: SUSTAINED_INFLAM
## 3675: SUSTAINED_INFLAM
## GOID include coefficient Stim effectfilter
## 1: CORE_ANTIVIRAL TRUE StimLPS:Time2h StimLPS TRUE
## 2: CORE_ANTIVIRAL TRUE StimLPS:Time4h StimLPS TRUE
## 3: CORE_ANTIVIRAL TRUE StimLPS:Time6h StimLPS TRUE
## 4: GO:0000288 TRUE StimLPS:Time2h StimLPS TRUE
## 5: GO:0000288 TRUE StimLPS:Time4h StimLPS TRUE
## ---
## 3671: PEAKED_INFLAM TRUE StimLPS:Time4h StimLPS FALSE
## 3672: PEAKED_INFLAM TRUE StimLPS:Time6h StimLPS FALSE
## 3673: SUSTAINED_INFLAM TRUE StimLPS:Time2h StimLPS TRUE
## 3674: SUSTAINED_INFLAM TRUE StimLPS:Time4h StimLPS TRUE
## 3675: SUSTAINED_INFLAM TRUE StimLPS:Time6h StimLPS TRUE
## variable value component
## 1: P 2.255322e-28 P
## 2: P 0.000000e+00 P
## 3: P 0.000000e+00 P
## 4: P 6.098448e-14 P
## 5: P 7.066308e-15 P
## ---
## 3671: include_sub 0.000000e+00 include
## 3672: include_sub 0.000000e+00 include
## 3673: include_sub 1.000000e+00 include
## 3674: include_sub 1.000000e+00 include
## 3675: include_sub 1.000000e+00 include
## TERM GOID include
## 1: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 2: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 3: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 4: activation of MAPKKK activity GO:0000185 TRUE
## 5: activation of MAPKKK activity GO:0000185 TRUE
## ---
## 4196: PEAKED_INFLAM PEAKED_INFLAM TRUE
## 4197: PEAKED_INFLAM PEAKED_INFLAM TRUE
## 4198: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## 4199: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## 4200: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## coefficient Stim effectfilter variable value
## 1: StimPIC:Time2h StimPIC FALSE P 2.300405e-01
## 2: StimPIC:Time4h StimPIC TRUE P 6.968623e-48
## 3: StimPIC:Time6h StimPIC TRUE P 2.253407e-192
## 4: StimPIC:Time2h StimPIC TRUE P 1.295313e-06
## 5: StimPIC:Time4h StimPIC TRUE P 2.507901e-01
## ---
## 4196: StimPIC:Time4h StimPIC FALSE include_sub 0.000000e+00
## 4197: StimPIC:Time6h StimPIC FALSE include_sub 0.000000e+00
## 4198: StimPIC:Time2h StimPIC TRUE include_sub 1.000000e+00
## 4199: StimPIC:Time4h StimPIC TRUE include_sub 1.000000e+00
## 4200: StimPIC:Time6h StimPIC TRUE include_sub 1.000000e+00
## component
## 1: P
## 2: P
## 3: P
## 4: P
## 5: P
## ---
## 4196: include
## 4197: include
## 4198: include
## 4199: include
## 4200: include
## TERM GOID include
## 1: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 2: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 3: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 4: activation of MAPKKK activity GO:0000185 TRUE
## 5: activation of MAPKKK activity GO:0000185 TRUE
## ---
## 4196: PEAKED_INFLAM PEAKED_INFLAM TRUE
## 4197: PEAKED_INFLAM PEAKED_INFLAM TRUE
## 4198: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## 4199: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## 4200: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## coefficient Stim effectfilter variable value
## 1: StimPIC:Time2h StimPIC FALSE P 2.300405e-01
## 2: StimPIC:Time4h StimPIC TRUE P 6.968623e-48
## 3: StimPIC:Time6h StimPIC TRUE P 2.253407e-192
## 4: StimPIC:Time2h StimPIC TRUE P 1.295313e-06
## 5: StimPIC:Time4h StimPIC TRUE P 2.507901e-01
## ---
## 4196: StimPIC:Time4h StimPIC FALSE include_sub 0.000000e+00
## 4197: StimPIC:Time6h StimPIC FALSE include_sub 0.000000e+00
## 4198: StimPIC:Time2h StimPIC TRUE include_sub 1.000000e+00
## 4199: StimPIC:Time4h StimPIC TRUE include_sub 1.000000e+00
## 4200: StimPIC:Time6h StimPIC TRUE include_sub 1.000000e+00
## component
## 1: P
## 2: P
## 3: P
## 4: P
## 5: P
## ---
## 4196: include
## 4197: include
## 4198: include
## 4199: include
## 4200: include
## TERM GOID include
## 1: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 2: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 3: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 4: ribosomal small subunit assembly GO:0000028 TRUE
## 5: ribosomal small subunit assembly GO:0000028 TRUE
## ---
## 5519: PEAKED_INFLAM PEAKED_INFLAM TRUE
## 5520: PEAKED_INFLAM PEAKED_INFLAM TRUE
## 5521: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## 5522: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## 5523: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## coefficient Stim effectfilter variable value
## 1: StimPAM:Time2h StimPAM FALSE P 5.450429e-04
## 2: StimPAM:Time4h StimPAM TRUE P 1.693595e-20
## 3: StimPAM:Time6h StimPAM TRUE P 2.878758e-98
## 4: StimPAM:Time2h StimPAM FALSE P 2.028658e-02
## 5: StimPAM:Time4h StimPAM TRUE P 2.348552e-07
## ---
## 5519: StimPAM:Time4h StimPAM TRUE include_sub 1.000000e+00
## 5520: StimPAM:Time6h StimPAM TRUE include_sub 1.000000e+00
## 5521: StimPAM:Time2h StimPAM TRUE include_sub 1.000000e+00
## 5522: StimPAM:Time4h StimPAM TRUE include_sub 1.000000e+00
## 5523: StimPAM:Time6h StimPAM TRUE include_sub 1.000000e+00
## component
## 1: P
## 2: P
## 3: P
## 4: P
## 5: P
## ---
## 5519: include
## 5520: include
## 5521: include
## 5522: include
## 5523: include
## TERM GOID include
## 1: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 2: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 3: CORE_ANTIVIRAL CORE_ANTIVIRAL TRUE
## 4: ribosomal small subunit assembly GO:0000028 TRUE
## 5: ribosomal small subunit assembly GO:0000028 TRUE
## ---
## 5519: PEAKED_INFLAM PEAKED_INFLAM TRUE
## 5520: PEAKED_INFLAM PEAKED_INFLAM TRUE
## 5521: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## 5522: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## 5523: SUSTAINED_INFLAM SUSTAINED_INFLAM TRUE
## coefficient Stim effectfilter variable value
## 1: StimPAM:Time2h StimPAM FALSE P 5.450429e-04
## 2: StimPAM:Time4h StimPAM TRUE P 1.693595e-20
## 3: StimPAM:Time6h StimPAM TRUE P 2.878758e-98
## 4: StimPAM:Time2h StimPAM FALSE P 2.028658e-02
## 5: StimPAM:Time4h StimPAM TRUE P 2.348552e-07
## ---
## 5519: StimPAM:Time4h StimPAM TRUE include_sub 1.000000e+00
## 5520: StimPAM:Time6h StimPAM TRUE include_sub 1.000000e+00
## 5521: StimPAM:Time2h StimPAM TRUE include_sub 1.000000e+00
## 5522: StimPAM:Time4h StimPAM TRUE include_sub 1.000000e+00
## 5523: StimPAM:Time6h StimPAM TRUE include_sub 1.000000e+00
## component
## 1: P
## 2: P
## 3: P
## 4: P
## 5: P
## ---
## 5519: include
## 5520: include
## 5521: include
## 5522: include
## 5523: include
## quartz_off_screen
## 2
## quartz_off_screen
## 2
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.2831
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.7317
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.7317
##
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.3218
##
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.401
##
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.2831
## [1] 377
## [1] 534
## [1] 193
## [1] 362
## quartz_off_screen
## 2
## quartz_off_screen
## 2
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6551
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.4775
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.4775
##
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6041
##
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.3993
##
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.6551
## quartz_off_screen
## 2
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.8058
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.8955
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.8955
##
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.5383
##
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.3324
##
## Estimating optimal shrinkage intensity lambda (correlation matrix): 0.8058
## quartz_off_screen
## 2