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ExperimentalDesign
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reset
2
votes
3
replies
1.1k
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Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 9 months ago by
swbarnes2
★ 1.4k • written 9 months ago by
Sam
• 0
2
votes
1
reply
713
views
edgeR with Successive Differences Contrast Coding?
hypothesisTesting
contrastCoding
edger
ExperimentalDesign
expressionDifferences
updated 15 months ago by
Gordon Smyth
51k • written 15 months ago by
Hannes
• 0
1
vote
1
reply
802
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 22 months ago by
ATpoint
★ 4.2k • written 22 months ago by
Mohamed
▴ 30
1
vote
2
replies
1.2k
views
How to properly use DESeq2 for an experiment
ExperimentalDesign
RNASeq
DifferentialExpression
DESeq2
updated 2.2 years ago by
Michael Love
42k • written 2.2 years ago by
Aurélien
• 0
1
vote
2
replies
1.0k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment
scater
ExperimentalDesign
scran
2.4 years ago
msn
▴ 10
1
vote
4
replies
1.5k
views
DiffBind analysis on ChIP-Seq qata and design matrix
ChIPSeq
DiffBind
ExperimentalDesign
3.5 years ago • updated 3.4 years ago
SFn
• 0
6 results • Page
1 of 1
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Lluís Revilla Sancho
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Michael Love
42k
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Leonardo Collado Torres
★ 1.1k
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Gordon Smyth
51k
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