Andras_RNASeq
Juan Steibel
11/11/2020
First summary of RNAseq expression
First let’s look at the size of our gene expression table and how many genes are expressed.
A total of 25232 genes are expressed.
#descriptive statistics
Counts of gene expression:
## total number of genes## [1] 35735## genes with expression##
## FALSE TRUE
## 10503 25232## [1] 25232 20Gene expresion and filtering of non-expressed transcripts 
## [1] 25232
## Sample labels## [1] mut mut mut mut mut mut mut mut mut mut wt wt wt wt wt wt wt wt wt
## [20] wt
## Levels: wt mutMore descriptive analyses
Here we prepare the matrices of gene expression and we look at the overall gene expression by sample
## [1] "DGEList"
## attr(,"package")
## [1] "edgeR"## [1] "counts" "samples"## Sample matrix of read count per million## result_mut10_count result_mut1_count
## MSTRG.21351|ENSCAFG00000018009 9.173737 11.70929
## MSTRG.1338|ENSCAFG00000000293 50.671234 43.16524
## MSTRG.14810|ENSCAFG00000013414 19.095176 17.42113
## MSTRG.18116|ENSCAFG00000015607 11.158024 12.60686
## MSTRG.11829|ENSCAFG00000012768 39.283148 49.08108
## result_mut2_count result_mut3_count
## MSTRG.21351|ENSCAFG00000018009 8.875232 12.23631
## MSTRG.1338|ENSCAFG00000000293 46.248574 46.33252
## MSTRG.14810|ENSCAFG00000013414 12.545160 15.63287
## MSTRG.18116|ENSCAFG00000015607 10.335714 10.97349
## MSTRG.11829|ENSCAFG00000012768 53.401188 31.52701
## result_mut4_count
## MSTRG.21351|ENSCAFG00000018009 9.760479
## MSTRG.1338|ENSCAFG00000000293 48.715246
## MSTRG.14810|ENSCAFG00000013414 19.738825
## MSTRG.18116|ENSCAFG00000015607 12.374893
## MSTRG.11829|ENSCAFG00000012768 31.982997## How many genes have at least nine samples with a count per million>9?## filtercpm
## FALSE TRUE
## 8288 16944## Observe outlier sample in MDS plot
## [1] "DGEList"
## attr(,"package")
## [1] "edgeR"Normalization and differential expression
## Disp = 0.05224 , BCV = 0.2286## Disp = 0.12638 , BCV = 0.3555
## Disp = 0.07945 , BCV = 0.2819
## Disp = 0.10205 , BCV = 0.3195
## Disp = 0.10156 , BCV = 0.3187
## Disp = 0.09984 , BCV = 0.316
## Disp = 0.07492 , BCV = 0.2737
## Disp = 0.07534 , BCV = 0.2745
## Disp = 0.08666 , BCV = 0.2944
## Disp = 0.06858 , BCV = 0.2619
## Disp = 0.07597 , BCV = 0.2756
## Disp = 0.07841 , BCV = 0.28
## Disp = 0.06899 , BCV = 0.2627
## Disp = 0.07537 , BCV = 0.2745
## Disp = 0.07869 , BCV = 0.2805
## Disp = 0.06883 , BCV = 0.2624
## Disp = 0.05465 , BCV = 0.2338
## Disp = 0.05019 , BCV = 0.224
## Disp = 0.04631 , BCV = 0.2152
## Disp = 0.05955 , BCV = 0.244
## Disp = 0.05528 , BCV = 0.2351
## Disp = 0.04617 , BCV = 0.2149
## Disp = 0.08127 , BCV = 0.2851
## Disp = 0.04773 , BCV = 0.2185
## Disp = 0.04172 , BCV = 0.2043
## Disp = 0.03961 , BCV = 0.199
## Disp = 0.04762 , BCV = 0.2182
## Disp = 0.03545 , BCV = 0.1883
## Disp = 0.03809 , BCV = 0.1952
## Disp = 0.05374 , BCV = 0.2318
## Disp = 0.03564 , BCV = 0.1888
## Disp = 0.04109 , BCV = 0.2027
## Disp = 0.03945 , BCV = 0.1986
## Disp = 0.04355 , BCV = 0.2087
## Disp = 0.03682 , BCV = 0.1919
## Disp = 0.03381 , BCV = 0.1839
## Disp = 0.04676 , BCV = 0.2162
## Disp = 0.03504 , BCV = 0.1872
## Disp = 0.03448 , BCV = 0.1857
## Disp = 0.04559 , BCV = 0.2135
## Disp = 0.04599 , BCV = 0.2144
## Disp = 0.0366 , BCV = 0.1913
## Disp = 0.03701 , BCV = 0.1924
## Disp = 0.0317 , BCV = 0.178
## Disp = 0.05382 , BCV = 0.232
## Disp = 0.03623 , BCV = 0.1903
## Disp = 0.0372 , BCV = 0.1929
## Disp = 0.03789 , BCV = 0.1947
## Disp = 0.0394 , BCV = 0.1985
## Disp = 0.07201 , BCV = 0.2683
Differential expression analysis
## Histogram of p-values has desired shape
## Number of DE genes at FDR < 0.10## [1] 486 4## top 10 DE genes## logFC logCPM PValue FDR
## ENSCAFG00000003496 -3.3038972 -0.2021082 3.707565e-23 6.282098e-19
## MSTRG.7226|ENSCAFG00000010008 2.0565905 1.4806904 5.004808e-20 4.240073e-16
## MSTRG.17992|ENSCAFG00000013691 2.6499301 0.7453387 8.927332e-16 5.042157e-12
## MSTRG.5659|ENSCAFG00000012022 0.8956423 6.3263964 1.370016e-14 5.803387e-11
## MSTRG.4426|ENSCAFG00000006134 1.1326055 5.2603432 2.827142e-13 9.580620e-10
## MSTRG.12343 -2.4334341 0.2925127 7.589864e-13 2.143378e-09
## MSTRG.15878|ENSCAFG00000011115 -0.8856482 3.1270307 1.152219e-12 2.789029e-09
## ENSCAFG00000008193 2.5480143 0.9699329 1.692369e-11 3.584437e-08
## MSTRG.21590|ENSCAFG00000019451 -2.1465517 5.8520372 4.476487e-11 8.427733e-08
## MSTRG.2571|ENSCAFG00000003504 1.4288768 3.5031490 5.584084e-11 9.461671e-08ADAMTS expression
## TS10 results## Coefficient: groupsmut
## logFC logCPM PValue FDR
## MSTRG.8241|ENSCAFG00000018557 -0.2704827 5.067586 0.02006312 0.2745044## TS17 results## Coefficient: groupsmut
## logFC logCPM PValue FDR
## MSTRG.12393|ENSCAFG00000010709 -0.8999529 4.846317 5.439333e-05 0.008458657Searchable table of gene expression
## [1] 486 4## genes with at least one ID## [1] 425 4## genes with multiple names## lnn
## 1 2 3 4
## 406 16 1 2## annotation table## [1] 402 5## total number of genes in DE## [1] 449