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baySeq
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0
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624
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Help with baySeq paired data analysis - error running 'getLikelihoods'
baySeq
2.7 years ago
sharvari gujja
▴ 40
0
votes
1
reply
2.9k
views
PCA analysis with 2 biological replicates
bayseq
PCA
5.8 years ago
bsad
• 0
2
votes
2
replies
1.3k
views
Setting up Experiment Design in baySeq
bayseq
updated 8.2 years ago by
Thomas J Hardcastle
▴ 180 • written 8.2 years ago by
adityabandla
▴ 10
0
votes
5
replies
1.7k
views
baySeq pairedData error
bayseq
updated 8.7 years ago by
Thomas J Hardcastle
▴ 180 • written 8.7 years ago by
amab424
• 0
0
votes
0
replies
1.5k
views
baySeq missing data
bayseq
missing data
9.6 years ago
k.w.lau
• 0
1
vote
5
replies
3.2k
views
baySeq issues and questions
bayseq
metagenomics
10.1 years ago • updated 9.9 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 10.2 years ago by
Gordon Smyth
52k • written 10.2 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 10.7 years ago by
Koji Kadota
▴ 10 • written 10.7 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 10.7 years ago by
Jianqiang SUN
▴ 10 • written 10.7 years ago by
Pankaj Agarwal
▴ 100
0
votes
2
replies
1.7k
views
Fwd: Paired Data Analysis in baySeq package
baySeq
baySeq
updated 10.9 years ago by
zhao shilin
▴ 60 • written 10.9 years ago by
Thomas J Hardcastle
▴ 180
0
votes
0
replies
1.2k
views
Paired Data Analysis in baySeq package
baySeq
baySeq
10.9 years ago
zhao shilin
▴ 60
0
votes
1
reply
1.3k
views
bayseq pair data
baySeq
baySeq
updated 11.3 years ago by
Thomas J Hardcastle
▴ 180 • written 11.3 years ago by
Guest User
★ 13k
0
votes
2
replies
3.0k
views
multi-mapped reads: Cufflinks + baySeq? edgeR?
GO
baySeq
GO
baySeq
11.8 years ago
Guest User
★ 13k
0
votes
2
replies
1.3k
views
weired bayseq results
baySeq
baySeq
12.1 years ago
Fatemehsadat Seyednasrollah
▴ 260
0
votes
0
replies
941
views
Bioconductor Digest, Vol 116, Issue 8
baySeq
baySeq
12.2 years ago
Thomas J Hardcastle
▴ 180
0
votes
0
replies
971
views
baySeq and samplesize factor
baySeq
baySeq
12.2 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 12.3 years ago by
Gordon Smyth
52k • written 12.3 years ago by
Elena Sorokin
▴ 160
0
votes
3
replies
1.3k
views
Help with plot comparison
baySeq
DEGseq
baySeq
DEGseq
12.8 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.2k
views
DEGseq help
baySeq
DEGseq
baySeq
DEGseq
12.9 years ago
Tina Asante Boahene
▴ 100
0
votes
0
replies
1.3k
views
FDR (False Discovery Rate)
baySeq
DEGseq
baySeq
DEGseq
12.9 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
12.9 years ago
Valerie Obenchain
★ 6.8k
0
votes
3
replies
1.5k
views
Help With RNA-seq
Normalization
edgeR
baySeq
Normalization
edgeR
baySeq
updated 12.9 years ago by
Valerie Obenchain
★ 6.8k • written 12.9 years ago by
Tina Asante Boahene
▴ 100
0
votes
1
reply
2.4k
views
TMM and calcNormFactors: Normalization in baySeq to match edgeR and DESeq
Normalization
Bayesian
edgeR
baySeq
DESeq
Normalization
Bayesian
edgeR
baySeq
DESeq
updated 13.1 years ago by
Smith, Hilary A
▴ 40 • written 13.1 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
13.1 years ago
Thomas J Hardcastle
▴ 180
0
votes
0
replies
2.4k
views
bayseq and edgeR for multi groups comparisons
edgeR
baySeq
edgeR
baySeq
13.1 years ago
Gordon Smyth
52k
0
votes
0
replies
1.5k
views
baySeq issues
edgeR
baySeq
edgeR
baySeq
13.4 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
13.7 years ago
Gordon Smyth
52k
0
votes
2
replies
1.2k
views
Bayseq vignette is missing
baySeq
baySeq
updated 14.5 years ago by
Chao-Jen Wong
▴ 580 • written 14.5 years ago by
Naomi Altman
★ 6.0k
28 results • Page
1 of 1
Recent ...
Replies
Comment: ISO a solution to rank-order introns by transcript
by
mat149
▴ 80
Hey, In revisiting this question, the following code works for the '+' strand. I am having issues with demarcating intron rank by transcri…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
Gordon Smyth
52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
anna.cot.anna.cot
▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
Tim Peters
▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw
by
Gordon Smyth
52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Votes
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Answer: nightmare to make custom txdb for genomes from ToxoDB
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