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bayseq
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0
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893
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Help with baySeq paired data analysis - error running 'getLikelihoods'
baySeq
3.7 years ago
sharvari gujja
▴ 40
0
votes
1
reply
3.5k
views
PCA analysis with 2 biological replicates
bayseq
PCA
6.8 years ago
bsad
• 0
2
votes
2
replies
1.5k
views
Setting up Experiment Design in baySeq
bayseq
updated 9.3 years ago by
Thomas J Hardcastle
▴ 180 • written 9.3 years ago by
adityabandla
▴ 10
0
votes
5
replies
2.0k
views
baySeq pairedData error
bayseq
updated 9.8 years ago by
Thomas J Hardcastle
▴ 180 • written 9.8 years ago by
amab424
• 0
0
votes
0
replies
1.7k
views
baySeq missing data
bayseq
missing data
10.7 years ago
k.w.lau
• 0
1
vote
5
replies
3.6k
views
baySeq issues and questions
bayseq
metagenomics
11.2 years ago • updated 11.0 years ago
lordbleys
• 0
1
vote
2
replies
1.5k
views
more complicated hypotheses than differential expression (with baySeq or a similar package)
bayseq
hypotheses
updated 11.2 years ago by
Gordon Smyth
53k • written 11.2 years ago by
Will Landau
• 0
0
votes
1
reply
2.0k
views
TCC::ERROR: Need the design matrix for GLM
DifferentialExpression
Normalization
Cancer
edgeR
baySeq
DESeq
EBSeq
TCC
Normalization
updated 11.8 years ago by
Koji Kadota
▴ 10 • written 11.8 years ago by
Gordon Smyth
53k
0
votes
1
reply
2.3k
views
TCC::ERROR: Need the design matrix for GLM.
DifferentialExpression
Normalization
Cancer
edgeR
baySeq
DESeq
EBSeq
TCC
Normalization
updated 11.8 years ago by
Jianqiang SUN
▴ 10 • written 11.8 years ago by
Pankaj Agarwal
▴ 100
0
votes
2
replies
1.9k
views
Fwd: Paired Data Analysis in baySeq package
baySeq
baySeq
updated 11.9 years ago by
zhao shilin
▴ 60 • written 11.9 years ago by
Thomas J Hardcastle
▴ 180
0
votes
0
replies
1.3k
views
Paired Data Analysis in baySeq package
baySeq
baySeq
11.9 years ago
zhao shilin
▴ 60
0
votes
1
reply
1.4k
views
bayseq pair data
baySeq
baySeq
updated 12.3 years ago by
Thomas J Hardcastle
▴ 180 • written 12.3 years ago by
Guest User
★ 13k
0
votes
2
replies
3.3k
views
multi-mapped reads: Cufflinks + baySeq? edgeR?
GO
baySeq
GO
baySeq
12.9 years ago
Guest User
★ 13k
0
votes
2
replies
1.6k
views
weired bayseq results
baySeq
baySeq
13.2 years ago
Fatemehsadat Seyednasrollah
▴ 260
0
votes
0
replies
1.1k
views
Bioconductor Digest, Vol 116, Issue 8
baySeq
baySeq
13.3 years ago
Thomas J Hardcastle
▴ 180
0
votes
0
replies
1.1k
views
baySeq and samplesize factor
baySeq
baySeq
13.3 years ago
Fatemehsadat Seyednasrollah
▴ 260
0
votes
1
reply
4.6k
views
RNA-seq analysis and two-way ANOVAs
edgeR
baySeq
DEGseq
DESeq
DEXSeq
edgeR
baySeq
DEGseq
DESeq
DEXSeq
updated 13.4 years ago by
Gordon Smyth
53k • written 13.4 years ago by
Elena Sorokin
▴ 160
0
votes
3
replies
1.6k
views
Help with plot comparison
baySeq
DEGseq
baySeq
DEGseq
13.9 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.4k
views
DEGseq help
baySeq
DEGseq
baySeq
DEGseq
13.9 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.5k
views
FDR (False Discovery Rate)
baySeq
DEGseq
baySeq
DEGseq
14.0 years ago
Tina Asante Boahene
▴ 100
0
votes
2
replies
1.6k
views
Help With RNA-seq
Annotation
Normalization
Kidney
edgeR
baySeq
Annotation
Normalization
Kidney
edgeR
baySeq
14.0 years ago
Valerie Obenchain
★ 6.8k
0
votes
3
replies
1.8k
views
Help With RNA-seq
Normalization
edgeR
baySeq
Normalization
edgeR
baySeq
updated 14.0 years ago by
Valerie Obenchain
★ 6.8k • written 14.0 years ago by
Tina Asante Boahene
▴ 100
0
votes
1
reply
2.7k
views
TMM and calcNormFactors: Normalization in baySeq to match edgeR and DESeq
Normalization
Bayesian
edgeR
baySeq
DESeq
Normalization
Bayesian
edgeR
baySeq
DESeq
updated 14.2 years ago by
Smith, Hilary A
▴ 40 • written 14.2 years ago by
Gordon Smyth
53k
0
votes
0
replies
1.4k
views
TMM and calcNormFactors: Normalization in baySeq to match, edgeR and DESeq (Smith, Hilary A)
Normalization
edgeR
baySeq
DESeq
Normalization
edgeR
baySeq
DESeq
14.2 years ago
Thomas J Hardcastle
▴ 180
0
votes
0
replies
2.6k
views
bayseq and edgeR for multi groups comparisons
edgeR
baySeq
edgeR
baySeq
14.2 years ago
Gordon Smyth
53k
0
votes
0
replies
1.6k
views
baySeq issues
edgeR
baySeq
edgeR
baySeq
14.5 years ago
Iain Gallagher
▴ 930
0
votes
0
replies
1.4k
views
RNA-Seq with multiple factors [was Informations about DESeq package]
RNASeq
edgeR
baySeq
DESeq
RNASeq
edgeR
baySeq
DESeq
14.7 years ago
Gordon Smyth
53k
0
votes
2
replies
1.4k
views
Bayseq vignette is missing
baySeq
baySeq
updated 15.6 years ago by
Chao-Jen Wong
▴ 580 • written 15.6 years ago by
Naomi Altman
★ 6.0k
28 results • Page
1 of 1
Recent ...
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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