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written 2.6 years ago by
marongiu.luigi
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written 2.6 years ago by
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Santiago Edilberto
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Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
by
Gordon Smyth
48k
I am telling you that
`LS_B.vs.NL_B`
is completely uninteresting.
You need instead to examine
`LS_Y.vs.NL_Y`
and
`LS_N.vs.NL_N`
separately.
Answer: Batch correction and repeated measures
by
Gordon Smyth
48k
You should just do a standard limma analysis as recommended in the previous posts.
```
design <- model.matrix(~0 + Sample.Type + batch)
i <…
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
Rockbar
•
0
When I apply the model.matrix approach for getting the contrasts, the code
> mod_mat <- model.matrix(design(dds), colData(dds))
> CondA.t…
Comment: DESeq2, results(dds, name = <reference>) interpretation results
by
Rockbar
•
0
Yes, I agree, the correct contrast setting is quite challenging. The vignette says
>contrast: a list of 2 character vectors: the names of…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.).
lengthScaledTPM puts back *in* the ge…
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