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bayseq
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643
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Help with baySeq paired data analysis - error running 'getLikelihoods'
baySeq
2.8 years ago
sharvari gujja
▴ 40
0
votes
1
reply
3.0k
views
PCA analysis with 2 biological replicates
bayseq
PCA
5.9 years ago
bsad
• 0
2
votes
2
replies
1.3k
views
Setting up Experiment Design in baySeq
bayseq
updated 8.3 years ago by
Thomas J Hardcastle
▴ 180 • written 8.3 years ago by
adityabandla
▴ 10
0
votes
5
replies
1.7k
views
baySeq pairedData error
bayseq
updated 8.8 years ago by
Thomas J Hardcastle
▴ 180 • written 8.8 years ago by
amab424
• 0
0
votes
0
replies
1.5k
views
baySeq missing data
bayseq
missing data
9.8 years ago
k.w.lau
• 0
1
vote
5
replies
3.2k
views
baySeq issues and questions
bayseq
metagenomics
10.2 years ago • updated 10.0 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 10.3 years ago by
Gordon Smyth
52k • written 10.3 years ago by
Will Landau
• 0
0
votes
1
reply
1.8k
views
TCC::ERROR: Need the design matrix for GLM
DifferentialExpression
Normalization
Cancer
edgeR
baySeq
DESeq
EBSeq
TCC
Normalization
updated 10.8 years ago by
Koji Kadota
▴ 10 • written 10.8 years ago by
Gordon Smyth
52k
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 10.8 years ago by
Jianqiang SUN
▴ 10 • written 10.8 years ago by
Pankaj Agarwal
▴ 100
0
votes
2
replies
1.7k
views
Fwd: Paired Data Analysis in baySeq package
baySeq
baySeq
updated 11.0 years ago by
zhao shilin
▴ 60 • written 11.0 years ago by
Thomas J Hardcastle
▴ 180
0
votes
0
replies
1.2k
views
Paired Data Analysis in baySeq package
baySeq
baySeq
11.0 years ago
zhao shilin
▴ 60
0
votes
1
reply
1.3k
views
bayseq pair data
baySeq
baySeq
updated 11.4 years ago by
Thomas J Hardcastle
▴ 180 • written 11.4 years ago by
Guest User
★ 13k
0
votes
2
replies
3.1k
views
multi-mapped reads: Cufflinks + baySeq? edgeR?
GO
baySeq
GO
baySeq
11.9 years ago
Guest User
★ 13k
0
votes
2
replies
1.3k
views
weired bayseq results
baySeq
baySeq
12.2 years ago
Fatemehsadat Seyednasrollah
▴ 260
0
votes
0
replies
954
views
Bioconductor Digest, Vol 116, Issue 8
baySeq
baySeq
12.3 years ago
Thomas J Hardcastle
▴ 180
0
votes
0
replies
984
views
baySeq and samplesize factor
baySeq
baySeq
12.3 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 12.4 years ago by
Gordon Smyth
52k • written 12.4 years ago by
Elena Sorokin
▴ 160
0
votes
3
replies
1.3k
views
Help with plot comparison
baySeq
DEGseq
baySeq
DEGseq
12.9 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.2k
views
DEGseq help
baySeq
DEGseq
baySeq
DEGseq
13.0 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.3k
views
FDR (False Discovery Rate)
baySeq
DEGseq
baySeq
DEGseq
13.0 years ago
Tina Asante Boahene
▴ 100
0
votes
2
replies
1.4k
views
Help With RNA-seq
Annotation
Normalization
Kidney
edgeR
baySeq
Annotation
Normalization
Kidney
edgeR
baySeq
13.0 years ago
Valerie Obenchain
★ 6.8k
0
votes
3
replies
1.5k
views
Help With RNA-seq
Normalization
edgeR
baySeq
Normalization
edgeR
baySeq
updated 13.0 years ago by
Valerie Obenchain
★ 6.8k • written 13.0 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 13.2 years ago by
Smith, Hilary A
▴ 40 • written 13.2 years ago by
Gordon Smyth
52k
0
votes
0
replies
1.2k
views
TMM and calcNormFactors: Normalization in baySeq to match, edgeR and DESeq (Smith, Hilary A)
Normalization
edgeR
baySeq
DESeq
Normalization
edgeR
baySeq
DESeq
13.2 years ago
Thomas J Hardcastle
▴ 180
0
votes
0
replies
2.4k
views
bayseq and edgeR for multi groups comparisons
edgeR
baySeq
edgeR
baySeq
13.2 years ago
Gordon Smyth
52k
0
votes
0
replies
1.5k
views
baySeq issues
edgeR
baySeq
edgeR
baySeq
13.5 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
13.8 years ago
Gordon Smyth
52k
0
votes
2
replies
1.2k
views
Bayseq vignette is missing
baySeq
baySeq
updated 14.6 years ago by
Chao-Jen Wong
▴ 580 • written 14.6 years ago by
Naomi Altman
★ 6.0k
28 results • Page
1 of 1
Recent ...
Replies
Answer: Selection of correct coefficients or contrasts in DESeq2
by
swbarnes2
★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry
by
Luca
• 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq?
by
Quang NN
▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot
by
ATpoint
★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq?
by
ATpoint
★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
Votes
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
Awards
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to
Aaron Lun
★ 28k
Popular Question
to
shepherl
4.1k
Popular Question
to
simon.andrews
• 0
Popular Question
to
Gordon Smyth
52k
Popular Question
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