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bayseq
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0
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695
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Help with baySeq paired data analysis - error running 'getLikelihoods'
baySeq
3.0 years ago
sharvari gujja
▴ 40
0
votes
1
reply
3.2k
views
PCA analysis with 2 biological replicates
bayseq
PCA
6.1 years ago
bsad
• 0
2
votes
2
replies
1.4k
views
Setting up Experiment Design in baySeq
bayseq
updated 8.6 years ago by
Thomas J Hardcastle
▴ 180 • written 8.6 years ago by
adityabandla
▴ 10
0
votes
5
replies
1.8k
views
baySeq pairedData error
bayseq
updated 9.0 years ago by
Thomas J Hardcastle
▴ 180 • written 9.0 years ago by
amab424
• 0
0
votes
0
replies
1.5k
views
baySeq missing data
bayseq
missing data
10.0 years ago
k.w.lau
• 0
1
vote
5
replies
3.3k
views
baySeq issues and questions
bayseq
metagenomics
10.5 years ago • updated 10.2 years ago
lordbleys
• 0
1
vote
2
replies
1.3k
views
more complicated hypotheses than differential expression (with baySeq or a similar package)
bayseq
hypotheses
updated 10.5 years ago by
Gordon Smyth
52k • written 10.5 years ago by
Will Landau
• 0
0
votes
1
reply
1.9k
views
TCC::ERROR: Need the design matrix for GLM
DifferentialExpression
Normalization
Cancer
edgeR
baySeq
DESeq
EBSeq
TCC
Normalization
updated 11.0 years ago by
Koji Kadota
▴ 10 • written 11.0 years ago by
Gordon Smyth
52k
0
votes
1
reply
2.1k
views
TCC::ERROR: Need the design matrix for GLM.
DifferentialExpression
Normalization
Cancer
edgeR
baySeq
DESeq
EBSeq
TCC
Normalization
updated 11.0 years ago by
Jianqiang SUN
▴ 10 • written 11.0 years ago by
Pankaj Agarwal
▴ 100
0
votes
2
replies
1.8k
views
Fwd: Paired Data Analysis in baySeq package
baySeq
baySeq
updated 11.2 years ago by
zhao shilin
▴ 60 • written 11.2 years ago by
Thomas J Hardcastle
▴ 180
0
votes
0
replies
1.2k
views
Paired Data Analysis in baySeq package
baySeq
baySeq
11.2 years ago
zhao shilin
▴ 60
0
votes
1
reply
1.3k
views
bayseq pair data
baySeq
baySeq
updated 11.6 years ago by
Thomas J Hardcastle
▴ 180 • written 11.6 years ago by
Guest User
★ 13k
0
votes
2
replies
3.1k
views
multi-mapped reads: Cufflinks + baySeq? edgeR?
GO
baySeq
GO
baySeq
12.2 years ago
Guest User
★ 13k
0
votes
2
replies
1.4k
views
weired bayseq results
baySeq
baySeq
12.4 years ago
Fatemehsadat Seyednasrollah
▴ 260
0
votes
0
replies
982
views
Bioconductor Digest, Vol 116, Issue 8
baySeq
baySeq
12.6 years ago
Thomas J Hardcastle
▴ 180
0
votes
0
replies
1.0k
views
baySeq and samplesize factor
baySeq
baySeq
12.6 years ago
Fatemehsadat Seyednasrollah
▴ 260
0
votes
1
reply
4.4k
views
RNA-seq analysis and two-way ANOVAs
edgeR
baySeq
DEGseq
DESeq
DEXSeq
edgeR
baySeq
DEGseq
DESeq
DEXSeq
updated 12.7 years ago by
Gordon Smyth
52k • written 12.7 years ago by
Elena Sorokin
▴ 160
0
votes
3
replies
1.4k
views
Help with plot comparison
baySeq
DEGseq
baySeq
DEGseq
13.2 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.3k
views
DEGseq help
baySeq
DEGseq
baySeq
DEGseq
13.2 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.3k
views
FDR (False Discovery Rate)
baySeq
DEGseq
baySeq
DEGseq
13.2 years ago
Tina Asante Boahene
▴ 100
0
votes
2
replies
1.5k
views
Help With RNA-seq
Annotation
Normalization
Kidney
edgeR
baySeq
Annotation
Normalization
Kidney
edgeR
baySeq
13.2 years ago
Valerie Obenchain
★ 6.8k
0
votes
3
replies
1.6k
views
Help With RNA-seq
Normalization
edgeR
baySeq
Normalization
edgeR
baySeq
updated 13.3 years ago by
Valerie Obenchain
★ 6.8k • written 13.3 years ago by
Tina Asante Boahene
▴ 100
0
votes
1
reply
2.5k
views
TMM and calcNormFactors: Normalization in baySeq to match edgeR and DESeq
Normalization
Bayesian
edgeR
baySeq
DESeq
Normalization
Bayesian
edgeR
baySeq
DESeq
updated 13.4 years ago by
Smith, Hilary A
▴ 40 • written 13.4 years ago by
Gordon Smyth
52k
0
votes
0
replies
1.3k
views
TMM and calcNormFactors: Normalization in baySeq to match, edgeR and DESeq (Smith, Hilary A)
Normalization
edgeR
baySeq
DESeq
Normalization
edgeR
baySeq
DESeq
13.4 years ago
Thomas J Hardcastle
▴ 180
0
votes
0
replies
2.4k
views
bayseq and edgeR for multi groups comparisons
edgeR
baySeq
edgeR
baySeq
13.4 years ago
Gordon Smyth
52k
0
votes
0
replies
1.5k
views
baySeq issues
edgeR
baySeq
edgeR
baySeq
13.7 years ago
Iain Gallagher
▴ 930
0
votes
0
replies
1.3k
views
RNA-Seq with multiple factors [was Informations about DESeq package]
RNASeq
edgeR
baySeq
DESeq
RNASeq
edgeR
baySeq
DESeq
14.0 years ago
Gordon Smyth
52k
0
votes
2
replies
1.3k
views
Bayseq vignette is missing
baySeq
baySeq
updated 14.9 years ago by
Chao-Jen Wong
▴ 580 • written 14.9 years ago by
Naomi Altman
★ 6.0k
28 results • Page
1 of 1
Recent ...
Replies
Comment: Differing results with DESeq2
by
JKim
• 0
I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for gene expressio…
Answer: CluserProfiler message "No gene can be mapped"
by
James W. MacDonald
68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE
by
James W. MacDonald
68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation
by
sergisayolspuig
▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2
by
cold.wolverine.arku
• 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
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