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baySeq
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0
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652
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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 8.4 years ago by
Thomas J Hardcastle
▴ 180 • written 8.4 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
10.3 years ago • updated 10.1 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
12.0 years ago
Guest User
★ 13k
0
votes
2
replies
1.4k
views
weired bayseq results
baySeq
baySeq
12.3 years ago
Fatemehsadat Seyednasrollah
▴ 260
0
votes
0
replies
960
views
Bioconductor Digest, Vol 116, Issue 8
baySeq
baySeq
12.4 years ago
Thomas J Hardcastle
▴ 180
0
votes
0
replies
993
views
baySeq and samplesize factor
baySeq
baySeq
12.4 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 12.5 years ago by
Gordon Smyth
52k • written 12.5 years ago by
Elena Sorokin
▴ 160
0
votes
3
replies
1.4k
views
Help with plot comparison
baySeq
DEGseq
baySeq
DEGseq
13.0 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
13.1 years ago
Valerie Obenchain
★ 6.8k
0
votes
3
replies
1.5k
views
Help With RNA-seq
Normalization
edgeR
baySeq
Normalization
edgeR
baySeq
updated 13.1 years ago by
Valerie Obenchain
★ 6.8k • written 13.1 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 13.3 years ago by
Smith, Hilary A
▴ 40 • written 13.3 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
13.3 years ago
Thomas J Hardcastle
▴ 180
0
votes
0
replies
2.4k
views
bayseq and edgeR for multi groups comparisons
edgeR
baySeq
edgeR
baySeq
13.3 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 14.7 years ago by
Chao-Jen Wong
▴ 580 • written 14.7 years ago by
Naomi Altman
★ 6.0k
28 results • Page
1 of 1
Recent ...
Replies
Answer: SingleR with multiple single cell references
by
Aaron Lun
★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies
by
ATpoint
★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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maltethodberg
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abadgerw
• 0
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to
Jim Nemesh
▴ 10
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Wolfgang Huber
★ 13k
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James W. MacDonald
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