Showing : Experimental Design • reset
6
votes
6
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4.3k
views
Limma multi-group analysis - General F-test
limma experimental design
updated 4.1 years ago by 51k • written 4.1 years ago by ▴ 10
0
votes
1
reply
705
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.1 years ago by 42k • written 5.1 years ago by • 0
1
vote
2
replies
825
views
Call DE genes on Unbalanced design with controls
edger experimental design
5.1 years ago timedreamer ▴ 10
0
votes
4
replies
998
views
DESeq2 analysis design - different individuals for all samples
deseq2 rnaseq model.matrix experimental design
5.6 years ago Maithê Barros ▴ 10
1
vote
9
replies
1.6k
views
shRNA-Seq analysis using edgeR
shrnaseq edger experimental design model.matrix
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ★ 1.5k
0
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0
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923
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Job: Postdoctoral Research Fellowship- reinforcement learning in biology- London
job bioinformatician job machine learning gene expression experimental design Job
5.8 years ago dezer ▴ 10
2
votes
6
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1.1k
views
DESeq2 Gene Expression Set up: Behavior vs Age
deseq2 experimental design
updated 5.8 years ago by 42k • written 5.8 years ago by • 0
4
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2
replies
1.1k
views
How does the function model.matrix (to define experimental design) really works ?
experimental design model.matrix edger
updated 6.3 years ago by ★ 7.9k • written 6.3 years ago by ▴ 20
1
vote
2
replies
1.4k
views
DESeq2 design & model matrix not full rank - am I nesting correctly?
deseq2 model matrix experimental design multiple factor design
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
0
votes
1
reply
3.1k
views
DESeq2 design model/contrasts question 3 level condition
deseq2 model design differential gene expression experimental design
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
6
votes
1
reply
11k
views
DESeq2 interaction term in two-factor design, which contrasts?
deseq2 experimental design interaction model
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 30
1
vote
2
replies
4.5k
views
Multiple comparisons for DE analysis with DESeq2
deseq2 mirna-seq experimental design differential expression
updated 7.2 years ago by ▴ 690 • written 7.2 years ago by ▴ 10
1
vote
2
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1.6k
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 7.3 years ago by ★ 28k • written 7.3 years ago by • 0
0
votes
1
reply
955
views
Genotypic difference design using deseq2
Deseq2 genotype experimental design
updated 7.4 years ago by 42k • written 7.4 years ago by ▴ 90
5
votes
2
replies
1.8k
views
DESeq2 design matrix for timecourse
deseq2 experimental design timecourse rnaseq model
updated 7.7 years ago by 42k • written 7.7 years ago by ▴ 20
2
votes
2
replies
1.3k
views
EdgeR experimental design matrix
edger differential gene expression experimental design
updated 8.1 years ago by ★ 28k • written 8.1 years ago by • 0
6
votes
1
reply
2.5k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 8.6 years ago by 42k • written 8.6 years ago by ▴ 60
5
votes
7
replies
2.1k
views
what conditions affect my gene (with limma?)
limma geo experimental design
updated 8.9 years ago by 51k • written 8.9 years ago by • 0
4
votes
3
replies
3.0k
views
DESeq2 - design for TCGA level 3 data
deseq2 tcga experimental design multiple factor design
updated 9.1 years ago by 42k • written 9.1 years ago by ▴ 40
1
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2
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1.7k
views
qRT-PCR Sample Maximization software analysis and proper experimental design advice
qPCR Sample Maximization Analysis Experimental Design qRT-PCR
updated 9.2 years ago by 51k • written 9.2 years ago by ▴ 450
0
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4
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2.0k
views
Question: DESeq2 nested design, multifactor test
deseq2 experimental design
9.2 years ago Shucong Li ▴ 60
21 results • Page 1 of 1
Recent ...
Replies
Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Answer: LRT test for different timepoints (one tissue types vs. many tissue types) by Michael Love 42k
No, this is a contrast of estimated coefficient (e.g. the Wald test).
Comment: Ranking the GSEA Results by Michael Love 42k
Got it. So then I'll take off DESeq2 as its mostly a downstream question. You may need to direct the fgsea developer to the thread. When yo…
Comment: Ranking the GSEA Results by V_Vibes • 0
I have actually used the "fgsea" Bioconductor package which is used for GSEA. Thanks for pointing that out. I have edited that in the origi…
Comment: Ranking the GSEA Results by V_Vibes • 0
The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am gett…
Votes
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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