Showing : Experimental Design • reset
6
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6
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4.8k
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Limma multi-group analysis - General F-test
limma experimental design
updated 4.4 years ago by 51k • written 4.4 years ago by ▴ 10
0
votes
1
reply
815
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.5 years ago by 42k • written 5.5 years ago by • 0
1
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2
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923
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Call DE genes on Unbalanced design with controls
edger experimental design
5.5 years ago timedreamer ▴ 10
0
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4
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1.1k
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DESeq2 analysis design - different individuals for all samples
deseq2 rnaseq model.matrix experimental design
6.0 years ago Maithê Barros ▴ 10
1
vote
9
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1.8k
views
shRNA-Seq analysis using edgeR
shrnaseq edger experimental design model.matrix
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ★ 1.5k
0
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0
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1.0k
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Job: Postdoctoral Research Fellowship- reinforcement learning in biology- London
job bioinformatician job machine learning gene expression experimental design Job
6.1 years ago dezer ▴ 10
2
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6
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1.3k
views
DESeq2 Gene Expression Set up: Behavior vs Age
deseq2 experimental design
updated 6.1 years ago by 42k • written 6.1 years ago by • 0
4
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2
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1.3k
views
How does the function model.matrix (to define experimental design) really works ?
experimental design model.matrix edger
updated 6.6 years ago by ★ 7.9k • written 6.6 years ago by ▴ 20
1
vote
2
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1.6k
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DESeq2 design & model matrix not full rank - am I nesting correctly?
deseq2 model matrix experimental design multiple factor design
updated 6.8 years ago by 42k • written 6.8 years ago by • 0
0
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1
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3.3k
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DESeq2 design model/contrasts question 3 level condition
deseq2 model design differential gene expression experimental design
updated 6.8 years ago by 42k • written 6.8 years ago by • 0
6
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1
reply
11k
views
DESeq2 interaction term in two-factor design, which contrasts?
deseq2 experimental design interaction model
updated 7.3 years ago by 42k • written 7.3 years ago by ▴ 30
1
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2
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4.7k
views
Multiple comparisons for DE analysis with DESeq2
deseq2 mirna-seq experimental design differential expression
updated 7.5 years ago by ▴ 690 • written 7.5 years ago by ▴ 10
1
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2
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1.7k
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 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
0
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1
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1.0k
views
Genotypic difference design using deseq2
Deseq2 genotype experimental design
updated 7.7 years ago by 42k • written 7.7 years ago by ▴ 90
5
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2
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2.0k
views
DESeq2 design matrix for timecourse
deseq2 experimental design timecourse rnaseq model
updated 8.0 years ago by 42k • written 8.0 years ago by ▴ 20
2
votes
2
replies
1.4k
views
EdgeR experimental design matrix
edger differential gene expression experimental design
updated 8.4 years ago by ★ 28k • written 8.4 years ago by • 0
6
votes
1
reply
2.6k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 8.9 years ago by 42k • written 8.9 years ago by ▴ 60
5
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7
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2.3k
views
what conditions affect my gene (with limma?)
limma geo experimental design
updated 9.2 years ago by 51k • written 9.2 years ago by • 0
4
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3
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3.1k
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DESeq2 - design for TCGA level 3 data
deseq2 tcga experimental design multiple factor design
updated 9.5 years ago by 42k • written 9.5 years ago by ▴ 40
1
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2
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1.8k
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qRT-PCR Sample Maximization software analysis and proper experimental design advice
qPCR Sample Maximization Analysis Experimental Design qRT-PCR
updated 9.5 years ago by 51k • written 9.5 years ago by ▴ 450
0
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4
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2.1k
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Question: DESeq2 nested design, multifactor test
deseq2 experimental design
9.5 years ago Shucong Li ▴ 60
21 results • Page 1 of 1
Recent ...
Replies
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Fahd • 0
Thanks for looking into this. This issue results in the incorrect usage of multiple ORA software including EnrichR.
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k
Yes, I understand the implications of replacing the `OrgDb` packages in release. Maybe an upload to the annotationHub or GitHub could be an…
Votes
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
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