Hi,
We're working on a RNA binding protein and want to figure out if it binds different RNAs in 2 different conditions. We did an immunoprecipitation (IP) for the protein and prepared the RNA that was linked to the protein for sequencing. Eventually we have 4 libraries: total RNA in condition A, RNAs in IP in condition A, total in condition B and IP in condition B.
I want to know which RNAs are more (or less) in the IP in condition A vs. B normalized by the total RNA in these conditions. I used LRT of DESeq2 like this:
ddseq <- DESeq(ddseq, test="LRT", full=~group+condition, reduced=~group)
where group is IP and total and condition is condition A and B. This should tell me if the condition influence the ratio between IP and Total.
What I'm missing is the size of the effect. I can get the p-value from the results but I couldn't figure out how to see the effect of condition a vs B on the IP/Total. I'd appreciate your help.
Thanks
We're working on a RNA binding protein and want to figure out if it binds different RNAs in 2 different conditions. We did an immunoprecipitation (IP) for the protein and prepared the RNA that was linked to the protein for sequencing. Eventually we have 4 libraries: total RNA in condition A, RNAs in IP in condition A, total in condition B and IP in condition B.
I want to know which RNAs are more (or less) in the IP in condition A vs. B normalized by the total RNA in these conditions. I used LRT of DESeq2 like this:
ddseq <- DESeq(ddseq, test="LRT", full=~group+condition, reduced=~group)
where group is IP and total and condition is condition A and B. This should tell me if the condition influence the ratio between IP and Total.
What I'm missing is the size of the effect. I can get the p-value from the results but I couldn't figure out how to see the effect of condition a vs B on the IP/Total. I'd appreciate your help.
Thanks
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