1 DESeq2
I compute Diff Expr Analysis with DESeq2, separately for each tissue (EPI and TROPHO).
1.1 MA-plots
The threshold used for a dot to be colored in red in the MA-plots is: p-value adjusted < 0.05.
1.1.1 EPIBLAST
Figure:
1.1.2 TROPHOBLAST
Figure:
I export the DE genes with 0.05, ordered by pvalue, to /home/sara/PhD/sequencing_projects/Btgh_injected_E7_SMARTSeq/analysis/DESeq/.
sessionInfo()## R version 4.1.3 (2022-03-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
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## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
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## locale:
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## [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
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## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
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## other attached packages:
## [1] dplyr_1.0.10 vsn_3.62.0
## [3] ggrepel_0.9.2 pheatmap_1.0.12
## [5] gridExtra_2.3 ggpubr_0.5.0
## [7] DESeq2_1.34.0 SummarizedExperiment_1.24.0
## [9] Biobase_2.54.0 MatrixGenerics_1.6.0
## [11] matrixStats_0.62.0 GenomicRanges_1.46.1
## [13] GenomeInfoDb_1.30.1 IRanges_2.28.0
## [15] S4Vectors_0.32.4 BiocGenerics_0.40.0
## [17] data.table_1.14.6 reshape2_1.4.4
## [19] ggplot2_3.4.0
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## loaded via a namespace (and not attached):
## [1] colorspace_2.0-3 ggsignif_0.6.4 XVector_0.34.0
## [4] rstudioapi_0.14 farver_2.1.1 affyio_1.64.0
## [7] bit64_4.0.5 AnnotationDbi_1.56.2 fansi_1.0.3
## [10] codetools_0.2-18 splines_4.1.3 cachem_1.0.6
## [13] geneplotter_1.72.0 knitr_1.40 jsonlite_1.8.3
## [16] broom_1.0.1 annotate_1.72.0 ashr_2.2-54
## [19] png_0.1-7 BiocManager_1.30.22 compiler_4.1.3
## [22] httr_1.4.4 backports_1.4.1 assertthat_0.2.1
## [25] Matrix_1.5-3 fastmap_1.1.0 limma_3.50.3
## [28] cli_3.4.1 htmltools_0.5.3 tools_4.1.3
## [31] gtable_0.3.1 glue_1.6.2 GenomeInfoDbData_1.2.7
## [34] affy_1.72.0 Rcpp_1.0.9 carData_3.0-5
## [37] jquerylib_0.1.4 vctrs_0.5.1 Biostrings_2.62.0
## [40] preprocessCore_1.56.0 xfun_0.35 stringr_1.4.1
## [43] lifecycle_1.0.3 irlba_2.3.5.1 rstatix_0.7.1
## [46] XML_3.99-0.12 zlibbioc_1.40.0 scales_1.2.1
## [49] parallel_4.1.3 RColorBrewer_1.1-3 yaml_2.3.6
## [52] memoise_2.0.1 sass_0.4.2 stringi_1.7.8
## [55] RSQLite_2.2.18 SQUAREM_2021.1 highr_0.9
## [58] genefilter_1.76.0 BiocParallel_1.28.3 truncnorm_1.0-8
## [61] rlang_1.0.6 pkgconfig_2.0.3 bitops_1.0-7
## [64] evaluate_0.18 lattice_0.20-45 invgamma_1.1
## [67] purrr_0.3.5 labeling_0.4.2 bit_4.0.5
## [70] tidyselect_1.2.0 plyr_1.8.8 magrittr_2.0.3
## [73] R6_2.5.1 generics_0.1.3 DelayedArray_0.20.0
## [76] DBI_1.1.3 pillar_1.8.1 withr_2.5.0
## [79] prettydoc_0.4.1 survival_3.2-13 KEGGREST_1.34.0
## [82] abind_1.4-5 RCurl_1.98-1.9 mixsqp_0.3-48
## [85] tibble_3.1.8 crayon_1.5.2 car_3.1-1
## [88] utf8_1.2.2 rmarkdown_2.18 locfit_1.5-9.6
## [91] grid_4.1.3 blob_1.2.3 digest_0.6.30
## [94] xtable_1.8-4 tidyr_1.2.1 munsell_0.5.0
## [97] bslib_0.4.1