DiffBind multi-tissue comparison
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lryrainche • 0
@c6dbd3de
Last seen 11 hours ago
United States

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:

  1. How should I set up my contrast or design to compare one tissue (Placenta) to multiple tissues (all labeled as "OtherTissues")?
  2. Is the current Condition column sufficient, or should I modify it?
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