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Normalisation
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reset
3
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2
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1.6k
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Sequencing depth before and aftr normalisation with DESEQ2 doesn't look as expected: Problem?
normalisation
DESEQ2
updated 4.4 years ago by
swbarnes2
★ 1.4k • written 4.4 years ago by
xavier
• 0
2
votes
2
replies
989
views
Double normalising when using sva and deseq2
DESeq2
Normalisation
Bulkrnaseq
Svaseq
19 months ago
BioinfGuru
▴ 70
1
vote
2
replies
937
views
Different regions for normalisation
DESeq2
median-of-ratios
normalisation
2.7 years ago
msrch
• 0
0
votes
3
replies
4.3k
views
Normalisation - Deseq2 vs StingTie-Ballgown
deseq2
StringTie
RNA-seq
normalisation
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
JindrichK
• 0
0
votes
7
replies
1.9k
views
DESEQ2 for circRNA normalisation
DESEQ2
circRNA
normalisation
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
zoe.ward
• 0
5 results • Page
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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