Showing : Deseq2 • reset
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DESeq2 rerun returns different results
DESeq2
4 hours ago wl1111 • 0
0
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1
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127
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 19 hours ago by 42k • written 1 day ago by • 0
0
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1
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99
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
2
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2
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336
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Handling biological replicates in DESeq2
DESeq2
updated 2 days ago by ★ 4.5k • written 3 days ago by • 0
5
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2
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25k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.8 years ago by ▴ 30
1
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6
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824
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 6 days ago by 42k • written 6 days ago by ▴ 10
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2
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293
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 8 days ago by • 0
4
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5
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532
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
10 days ago • updated 9 days ago LuciaNhu • 0
0
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1
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334
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Average expression of genes across replicates
DESeq2
updated 12 days ago by ★ 4.5k • written 13 days ago by • 0
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0
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87
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
15 days ago info ▴ 10
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10
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1.2k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
16 days ago • updated 9 days ago Denise • 0
0
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1
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298
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Deseq to output continous sequencing data
DESeq2
updated 17 days ago by 42k • written 4 weeks ago by • 0
1
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4
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699
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Adjusted p-values become NA when sub-setting samples
DESeq2
5 weeks ago • updated 8 days ago txema.heredia • 0
3
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3
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798
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 19 days ago by • 0
0
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2
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299
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 23 days ago by • 0
0
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1
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253
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 24 days ago by 42k • written 24 days ago by • 0
2
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3
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970
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Analysis of large RNA-Seq Datasets
DESeq2
updated 26 days ago by 42k • written 27 days ago by • 0
1
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4
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699
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DESeq2 - interactions when using factors concatenated into group
DESeq2
28 days ago • updated 20 days ago boczniak767 ▴ 740
0
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1
reply
168
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
28 days ago JY • 0
0
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1
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250
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 29 days ago by 42k • written 29 days ago by • 0
0
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2
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179
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how to extract expression matrix post deseq2
DESeq2
written 29 days ago by • 0
0
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2
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172
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Using Normalized Counts in DESeq2
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
1
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2
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220
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When running contrasts, does it use normalized read counts?
DESeq2
4 weeks ago Katherine • 0
0
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1
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177
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 4 weeks ago by ★ 1.4k • written 4 weeks ago by • 0
3
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4
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437
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
4 weeks ago Eva ▴ 10
1
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4
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453
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 29 days ago by ★ 4.5k • written 6 weeks ago by • 0
0
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1
reply
159
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
3
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11
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675
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 5 weeks ago by • 0
2
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4
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370
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
5 weeks ago jihoon.kim.1495 ▴ 10
0
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6
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759
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 19 days ago by 42k • written 5 weeks ago by • 0
5
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4
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416
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 5 weeks ago by ★ 4.5k • written 6 weeks ago by • 0
0
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2
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255
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
5 weeks ago paul.meraner • 0
0
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0
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169
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
5 weeks ago • updated 15 days ago info ▴ 10
0
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5
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511
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heatmap with batch effect
DESeq2 BatchEffect
5 weeks ago tothuhien • 0
0
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2
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333
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
1
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1
reply
239
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
1
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1
reply
221
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 6 weeks ago by ★ 4.5k • written 6 weeks ago by • 0
1
vote
1
reply
308
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 6 weeks ago by ★ 4.5k • written 6 weeks ago by • 0
1
vote
2
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422
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 6 weeks ago by 42k • written 7 weeks ago by ▴ 10
0
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2
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680
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 6 weeks ago by 42k • written 7 weeks ago by • 0
1
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2
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465
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 6 weeks ago by 42k • written 8 weeks ago by ▴ 10
1
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6
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669
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 26 days ago by ★ 4.5k • written 7 weeks ago by • 0
0
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1
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277
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 7 weeks ago by 42k • written 8 weeks ago by • 0
17
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9
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7.0k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 8 weeks ago by 67k • written 8.5 years ago by ▴ 10
0
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1
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270
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
0
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2
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491
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 9 weeks ago by ★ 1.4k • written 10 weeks ago by • 0
0
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5
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1.6k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 3.5 years ago by • 0
3
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6
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1.4k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 9 weeks ago by 42k • written 10 weeks ago by • 0
3
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6
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27k
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Deseq: What does "BaseMean" mean?
deseq2
written 6.2 years ago by • 0
0
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2
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859
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 10 weeks ago by ★ 1.4k • written 11 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model by abadgerw • 0
@gabrielhoffman any insight?
Comment: makeContrastsDream for Interaction by abadgerw • 0
@gabrielhoffman any insight?
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta by Michael Love 42k
That is the rows that did converge.
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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