The editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: DESeq2 for ChIP-seq
gravatar for bioinfo
6 months ago by
bioinfo0 wrote:

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? 

diffbind deseq2 • 125 views
ADD COMMENTlink modified 6 months ago by Michael Love21k • written 6 months ago by bioinfo0
Answer: DESeq2 for ChIP-seq
gravatar for Michael Love
6 months ago by
Michael Love21k
United States
Michael Love21k wrote:

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

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.

ADD COMMENTlink written 6 months ago by Michael Love21k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 269 users visited in the last hour