DESeq2 for ChIP-seq
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@bioinfo-12782
Last seen 3 months ago
United States

I have ChIP-seq datasets as the following:

 

  Cell Type Condtion
1 A Input WT
2 A Pulldown WT
3 B Input WT
4 B Pulldown WT
5 C Input MT
6 C Pulldown MT
7 D Input MT
8 D Pulldown MT

 I would like to find differential region of pulldown between WT and MT in condition after controlling individual cells and types. I thought the design formula: ~ Cell + Type + Condition + Type*Condition. However, it generated "not full rank" error. When I tried to nested formula such as ~ Cell + Cell*Type + Cell *Condition, it still generated "not full rank" error. It only works with ~ Type + Condition + Type*Condition where I cannot block cell effect. Could anyone help me? 

deseq2 diffbind • 338 views
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@mikelove
Last seen 23 hours ago
United States

Cell is confounded with condition, so you need to follow this advice:

http://master.bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#group-specific-condition-effects-individuals-nested-within-groups

This advice includes making a new column, cell.nested which will take only values A and B (C => A and D => B). This will accomplish what you want but will avoid the error. It's simply a re-coding trick, the two cells in the two conditions will not be treated as identical because you have the condition:cell interaction.

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