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Hi,
Im working on a ChIP-seq project analyzing H3K27ac marks across multiple tissues. I have the following sample sheet (simplified) for DiffBind:
| SampleID | Tissue | Factor | Condition | Replicate |
|---|---|---|---|---|
| H3K27ac_adipose_r1 | adipose | H3K27ac | OtherTissues | r1 |
| H3K27ac_adipose_r2 | adipose | H3K27ac | OtherTissues | r2 |
| H3K27ac_cerebellum_r1 | cerebellum | H3K27ac | OtherTissues | r1 |
| H3K27ac_cerebellum_r2 | cerebellum | H3K27ac | OtherTissues | r2 |
| H3K27ac_cortex_r1 | cortex | H3K27ac | OtherTissues | r1 |
| H3K27ac_cortex_r2 | cortex | H3K27ac | OtherTissues | r2 |
| H3K27ac_Cecum_r1 | Cecum | H3K27ac | OtherTissues | r1 |
| H3K27ac_Cecum_r2 | Cecum | H3K27ac | OtherTissues | r2 |
| H3K27ac_Colon_r1 | Colon | H3K27ac | OtherTissues | r1 |
| H3K27ac_Colon_r2 | Colon | H3K27ac | OtherTissues | r2 |
| H3K27ac_Duodenum_r1 | Duodenum | H3K27ac | OtherTissues | r1 |
| H3K27ac_Duodenum_r2 | Duodenum | H3K27ac | OtherTissues | r2 |
| H3K27ac_hypothalamus_r1 | hypothalamus | H3K27ac | OtherTissues | r1 |
| H3K27ac_hypothalamus_r2 | hypothalamus | H3K27ac | OtherTissues | r2 |
| H3K27ac_Ileum_r1 | Ileum | H3K27ac | OtherTissues | r1 |
| H3K27ac_Ileum_r2 | Ileum | H3K27ac | OtherTissues | r2 |
| H3K27ac_Jejunum_r1 | Jejunum | H3K27ac | OtherTissues | r1 |
| H3K27ac_Jejunum_r2 | Jejunum | H3K27ac | OtherTissues | r2 |
| H3K27ac_liver_r1 | liver | H3K27ac | OtherTissues | r1 |
| H3K27ac_liver_r2 | liver | H3K27ac | OtherTissues | r2 |
| H3K27ac_lung_r1 | lung | H3K27ac | OtherTissues | r1 |
| H3K27ac_lung_r2 | lung | H3K27ac | OtherTissues | r2 |
| H3K27ac_Placenta_r1 | Placenta | H3K27ac | Placenta | r1 |
| H3K27ac_Placenta_r2 | Placenta | H3K27ac | Placenta | r2 |
| H3K27ac_spleen_r1 | spleen | H3K27ac | OtherTissues | r1 |
| H3K27ac_spleen_r2 | spleen | H3K27ac | OtherTissues | r2 |
| H3K27ac_Stomach_r1 | Stomach | H3K27ac | OtherTissues | r1 |
| H3K27ac_Stomach_r2 | Stomach | H3K27ac | OtherTissues | r2 |
I would like to perform a differential binding analysis using DiffBind in R, comparing Placenta against all other tissues. My question is:
- How should I set up my contrast or design to compare one tissue (Placenta) to multiple tissues (all labeled as "OtherTissues")?
- Is the current
Conditioncolumn sufficient, or should I modify it?
