Hi, I have an experimental design where I have groups (sham and SA) and treatments (control and treated) with paired samples. It looks like this:
| Samples | Group | Treatment | Mice | Mice.nested |
|---|---|---|---|---|
| A1 | Sham | Control | A | A |
| ----------- | --------- | ------------- | ------- | ---------------- |
| A2 | Sham | Control | B | B |
| ----------- | --------- | ------------- | ------- | ---------------- |
| A3 | Sham | Control | C | C |
| ----------- | --------- | ------------- | ------- | ---------------- |
| A4 | Sham | Control | D | D |
| ----------- | --------- | ------------- | ------- | ---------------- |
| A5 | Sham | Control | E | E |
| ----------- | --------- | ------------- | ------- | ---------------- |
| B1 | Sham | Treated | A | A |
| ----------- | --------- | ------------- | ------- | ---------------- |
| B2 | Sham | Treated | B | B |
| ----------- | --------- | ------------- | ------- | ---------------- |
| B3 | Sham | Treated | C | C |
| ----------- | --------- | ------------- | ------- | ---------------- |
| B4 | Sham | Treated | D | D |
| ----------- | --------- | ------------- | ------- | ---------------- |
| B5 | Sham | Treated | E | E |
| ----------- | --------- | ------------- | ------- | ---------------- |
| C1 | SA | Control | F | A |
| ----------- | --------- | ------------- | ------- | ---------------- |
| C2 | SA | Control | G | B |
| ----------- | --------- | ------------- | ------- | ---------------- |
| C3 | SA | Control | H | C |
| ----------- | --------- | ------------- | ------- | ---------------- |
| C4 | SA | Control | I | D |
| ----------- | --------- | ------------- | ------- | ---------------- |
| C5 | SA | Control | J | E |
| ----------- | --------- | ------------- | ------- | ---------------- |
| D1 | SA | Treated | F | A |
| ----------- | --------- | ------------- | ------- | ---------------- |
| D2 | SA | Treated | G | B |
| ----------- | --------- | ------------- | ------- | ---------------- |
| D3 | SA | Treated | H | C |
| ----------- | --------- | ------------- | ------- | ---------------- |
| D4 | SA | Treated | I | D |
| ----------- | --------- | ------------- | ------- | ---------------- |
| D5 | SA | Treated | J | E |
| ----------- | --------- | ------------- | ------- | ---------------- |
I would like to know what are the differentially expressed genes within groups and between treatments, and I think the following would give me that:
design= ~ Group + Group:Mice.nested + Group:Treatment
Extract Sham-control vs Sham-treated
results(dds, name = "GroupSham.TreatmentTreated", test="Wald", alpha=0.05)
Extract SA-control vs SA-treated
results(dds, name = "GroupSa.TreatmentTreated", test="Wald", alpha=0.05)
Assuming everything I did at this point is correct (which could not be), how would I extract the genes that are changing between groups within treatments (Sham-vs-SA_control and Sham-vs-SA_treated) Thanks in advance
```> sessionInfo() R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DESeq2_1.36.0 SummarizedExperiment_1.26.1 Biobase_2.56.0 MatrixGenerics_1.8.1 matrixStats_0.62.0
[6] GenomicRanges_1.48.0 GenomeInfoDb_1.32.4 IRanges_2.30.1 S4Vectors_0.34.0 BiocGenerics_0.42.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 locfit_1.5-9.6 lattice_0.20-45 png_0.1-7 Biostrings_2.64.1 assertthat_0.2.1
[7] utf8_1.2.2 R6_2.5.1 RSQLite_2.2.18 httr_1.4.4 ggplot2_3.3.6 pillar_1.8.1
[13] zlibbioc_1.42.0 rlang_1.0.6 rstudioapi_0.14 annotate_1.74.0 blob_1.2.3 Matrix_1.4-1
[19] splines_4.2.1 BiocParallel_1.30.4 geneplotter_1.74.0 RCurl_1.98-1.9 bit_4.0.4 munsell_0.5.0
[25] DelayedArray_0.22.0 compiler_4.2.1 pkgconfig_2.0.3 tidyselect_1.2.0 KEGGREST_1.36.3 tibble_3.1.8
[31] GenomeInfoDbData_1.2.8 codetools_0.2-18 XML_3.99-0.11 fansi_1.0.3 crayon_1.5.2 dplyr_1.0.10
[37] bitops_1.0-7 grid_4.2.1 xtable_1.8-4 gtable_0.3.1 lifecycle_1.0.3 DBI_1.1.3
[43] magrittr_2.0.3 scales_1.2.1 cli_3.4.1 cachem_1.0.6 XVector_0.36.0 genefilter_1.78.0
[49] generics_0.1.3 vctrs_0.4.2 cowplot_1.1.1 RColorBrewer_1.1-3 tools_4.2.1 bit64_4.0.5
[55] glue_1.6.2 parallel_4.2.1 fastmap_1.1.0 survival_3.3-1 AnnotationDbi_1.58.0 colorspace_2.0-3
[61] memoise_2.0.1 ```
