Hi all,
Is is possible to use a nested model in DESeq2 or EdgeR??
I have 3 treatments (evolution lines), but each treatment was performed in 4 replicate lines.
My experimental design is as follows:
TmtA x 4 replicate lines X 3 biological replicates sequenced in each replicate line
TmtB x 4 replicate lines X 3 biological replicates sequenced in each replicate line
TmtC x 4 replicate lines X 3 biological replicates sequenced in each replicate line
This has given me a total of 36 libraries.
My main interest is the difference between treatments, but I also want to take the independence of these 4 replicate lines into account while keeping them nested within their treatment. Is there an easy way to incorporate this in DESeqDataSeqFromMatrix (or similar, this is what I'm using now)?
Thanks.
Alice
Is is possible to use a nested model in DESeq2 or EdgeR??
I have 3 treatments (evolution lines), but each treatment was performed in 4 replicate lines.
My experimental design is as follows:
TmtA x 4 replicate lines X 3 biological replicates sequenced in each replicate line
TmtB x 4 replicate lines X 3 biological replicates sequenced in each replicate line
TmtC x 4 replicate lines X 3 biological replicates sequenced in each replicate line
This has given me a total of 36 libraries.
My main interest is the difference between treatments, but I also want to take the independence of these 4 replicate lines into account while keeping them nested within their treatment. Is there an easy way to incorporate this in DESeqDataSeqFromMatrix (or similar, this is what I'm using now)?
Thanks.
Alice
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