Showing : experimental design • reset
1
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9
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1.5k
views
shRNA-Seq analysis using edgeR
shrnaseq edger experimental design model.matrix
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ★ 1.5k
5
votes
7
replies
2.0k
views
what conditions affect my gene (with limma?)
limma geo experimental design
updated 8.7 years ago by 50k • written 8.7 years ago by • 0
6
votes
6
replies
4.1k
views
Limma multi-group analysis - General F-test
limma experimental design
updated 3.9 years ago by 50k • written 3.9 years ago by ▴ 10
2
votes
6
replies
1.1k
views
DESeq2 Gene Expression Set up: Behavior vs Age
deseq2 experimental design
updated 5.6 years ago by 41k • written 5.6 years ago by • 0
0
votes
4
replies
954
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DESeq2 analysis design - different individuals for all samples
deseq2 rnaseq model.matrix experimental design
5.5 years ago Maithê Barros ▴ 10
0
votes
4
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2.0k
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Question: DESeq2 nested design, multifactor test
deseq2 experimental design
9.0 years ago Shucong Li ▴ 60
4
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3
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2.9k
views
DESeq2 - design for TCGA level 3 data
deseq2 tcga experimental design multiple factor design
updated 9.0 years ago by 41k • written 9.0 years ago by ▴ 40
1
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2
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1.6k
views
qRT-PCR Sample Maximization software analysis and proper experimental design advice
qPCR Sample Maximization Analysis Experimental Design qRT-PCR
updated 9.0 years ago by 50k • written 9.0 years ago by ▴ 450
2
votes
2
replies
1.3k
views
EdgeR experimental design matrix
edger differential gene expression experimental design
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
5
votes
2
replies
1.8k
views
DESeq2 design matrix for timecourse
deseq2 experimental design timecourse rnaseq model
updated 7.5 years ago by 41k • written 7.5 years ago by ▴ 20
1
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2
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1.5k
views
Trying to design a model(s) for a two factor RNA-seq experimental analysis in EdgeR with interaction
EdgeR RNAseq experimental design glm
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
1
vote
2
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4.4k
views
Multiple comparisons for DE analysis with DESeq2
deseq2 mirna-seq experimental design differential expression
updated 7.0 years ago by ▴ 680 • written 7.0 years ago by ▴ 10
1
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2
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1.4k
views
DESeq2 design & model matrix not full rank - am I nesting correctly?
deseq2 model matrix experimental design multiple factor design
updated 6.3 years ago by 41k • written 6.3 years ago by • 0
4
votes
2
replies
1.1k
views
How does the function model.matrix (to define experimental design) really works ?
experimental design model.matrix edger
updated 6.1 years ago by ★ 7.9k • written 6.1 years ago by ▴ 20
1
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2
replies
799
views
Call DE genes on Unbalanced design with controls
edger experimental design
5.0 years ago timedreamer ▴ 10
6
votes
1
reply
11k
views
DESeq2 interaction term in two-factor design, which contrasts?
deseq2 experimental design interaction model
updated 6.8 years ago by 41k • written 6.8 years ago by ▴ 30
0
votes
1
reply
929
views
Genotypic difference design using deseq2
Deseq2 genotype experimental design
updated 7.2 years ago by 41k • written 7.2 years ago by ▴ 90
6
votes
1
reply
2.5k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 8.4 years ago by 41k • written 8.4 years ago by ▴ 60
0
votes
1
reply
679
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
0
votes
1
reply
2.9k
views
DESeq2 design model/contrasts question 3 level condition
deseq2 model design differential gene expression experimental design
updated 6.3 years ago by 41k • written 6.3 years ago by • 0
0
votes
0
replies
898
views
Job: Postdoctoral Research Fellowship- reinforcement learning in biology- London
job bioinformatician job machine learning gene expression experimental design Job
5.6 years ago dezer ▴ 10
21 results • Page 1 of 1
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Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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