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ExperimentalDesign
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2
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3
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821
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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
2
votes
1
reply
650
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
714
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
Mohamed
▴ 30
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
42k • written 24 months ago by
Aurélien
• 0
1
vote
2
replies
927
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
4
replies
1.3k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq
DiffBind
ExperimentalDesign
3.2 years ago
SFn
• 0
6 results • Page
1 of 1
Recent ...
Replies
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Mike Smith
★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results
by
ATpoint
★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data
by
ATpoint
★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
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