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ExperimentalDesign
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reset
1
vote
4
replies
1.3k
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DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq
DiffBind
ExperimentalDesign
3.2 years ago
SFn
• 0
2
votes
3
replies
805
views
Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 6 months ago by
swbarnes2
★ 1.3k • written 6 months ago by
Sam
• 0
1
vote
2
replies
925
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment
scater
ExperimentalDesign
scran
2.2 years ago
msn
▴ 10
1
vote
2
replies
1.1k
views
How to properly use DESeq2 for an experiment
ExperimentalDesign
RNASeq
DifferentialExpression
DESeq2
updated 24 months ago by
Michael Love
41k • written 24 months ago by
Aurélien
• 0
2
votes
1
reply
647
views
edgeR with Successive Differences Contrast Coding?
hypothesisTesting
contrastCoding
edger
ExperimentalDesign
expressionDifferences
updated 12 months ago by
Gordon Smyth
50k • written 12 months ago by
Hannes
• 0
1
vote
1
reply
710
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 19 months ago by
ATpoint
★ 4.1k • written 19 months ago by
Mohamed
▴ 30
6 results • Page
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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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