User: silvia.paolucci81

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Comment: C: design model matrix for nested factors (edgeR)
... Hi Aaron, thanks again for your comment. Yes, my design.temp is constructed using target$sample. Indeed the dispersions are quite high, this is why I don' t think pooling is the best option. However, at the moment it looks like it is the best I can do using edgeR. When I look at the heatmap of the s ...
written 4.7 years ago by silvia.paolucci810
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Comment: C: design model matrix for nested factors (edgeR)
... Hi Aaron, thank you very much for your suggestion! I am trying to do what you suggested and it looks like it's working. I thought about pooling the technical replicates, but I was not sure at which point I was supposed to pool.  And this is what I get when I check the NB dispersions summary(d.te ...
written 4.7 years ago by silvia.paolucci810
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design model matrix for nested factors (edgeR)
... Dear all,  I have a question on how to design the model matrix to properly analyze my RNAseq data. Here the summary of my data: I have two conditions (young and old). In each condition I have 3 biological replicates (sample) and each biological replicate is replicated twice (technical replicate), ...
edger design matrix model matrix written 4.7 years ago by silvia.paolucci810 • updated 4.7 years ago by Aaron Lun25k

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Popular Question 4.6 years ago, created a question with more than 1,000 views. For design model matrix for nested factors (edgeR)

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