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Answer: Batch effect adjust in model matrix
by
ATpoint
★
3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
Oh, I see.
If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`.
So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Christian
•
0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq.
The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Michael Love
40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline:
https://nf-co.re/rnaseq
You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
by
Christian
•
0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly.
However, further I´m…
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