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no replicates
•
reset
0
votes
0
replies
1.1k
views
MethylSig is not giving DMRs with no replicates
methylsig
no replicates
dmr
7.5 years ago
nilaycan
• 0
1
vote
5
replies
3.9k
views
steps to get up and down regulated genes using DESeq2
deseq2
without replicate
no replicates
updated 7.7 years ago by
Michael Love
43k • written 7.7 years ago by
Tony
• 0
4
votes
9
replies
12k
views
DESeq2, no replicate
deseq2
no replicates
high p-adj values
updated 3.5 years ago by
Michael Love
43k • written 8.3 years ago by
Mahtetie
• 0
4
votes
8
replies
2.9k
views
Advice regarding RNAseq data with no replicates, best approach to accomplish fold-change
rnaseq
edger
DGE
no replicates
8.4 years ago
Stefany Solano
• 0
2
votes
1
reply
1.7k
views
diffHiC with no biological replicates?
diffhic
estimate dispersion value
glm
no replicates
deseq
updated 8.8 years ago by
Aaron Lun
★ 29k • written 8.8 years ago by
hwick1
▴ 20
5
votes
7
replies
5.7k
views
Differential binding of ATAC-seq data with no replicates
ATAC
differential binding analysis
no replicates
DEseq2
chromatin
8.8 years ago
BioinfGuru
▴ 70
6 results • Page
1 of 1
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Replies
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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