Showing : DESeq2 • reset
5
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DESeq2 model - How to test case/control time course model when taking account within sample variability?
deseq2 multiple time points time course casecontrol model design
updated 25 days ago by • 0 • written 7.8 years ago by ▴ 10
34
votes
29
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16k
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[DESeq2] time series strain-specific differences over time
deseq2 timecourse
updated 7 months ago by 43k • written 10.1 years ago by ▴ 130
38
votes
23
replies
17k
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DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
10.6 years ago • updated 5 weeks ago Michael Love 43k
10
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20
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24k
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Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
deseq2 batch effect batch
updated 6 months ago by 68k • written 5.9 years ago by ▴ 30
6
votes
19
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4.8k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 12 months ago by • 0 • written 5.6 years ago by ▴ 10
6
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15
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1.9k
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Deseq2 design formula and analysis with internal controls
DESeq2
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
4
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12
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1.4k
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DGE with a Continuous Variable
DESeq2 model
updated 9 months ago by 43k • written 9 months ago by • 0
16
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12
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8.6k
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Diffbind: edgeR or DESeq2 ?
diffbind medip-seq edger deseq2
updated 7 months ago by • 0 • written 9.1 years ago by ▴ 60
4
votes
11
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1.1k
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
8 months ago • updated 7 months ago boczniak767 ▴ 740
17
votes
11
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40k
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DESeq2 and shrinkage of log2 fold changes
deseq2
updated 10 months ago by 43k • written 9.3 years ago by ▴ 100
0
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11
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1.9k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 23 days ago by • 0 • written 5 months ago by • 0
3
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11
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1.1k
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 6 months ago by • 0
0
votes
10
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1.6k
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Two treatments, one control
DESeq2 stageR
9 months ago alephreish • 0
8
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9
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15k
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 7 hours ago by • 0 • written 8.7 years ago by ▴ 20
17
votes
9
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7.6k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7 months ago by 68k • written 8.9 years ago by ▴ 10
1
vote
9
replies
1.1k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 4 months ago by ▴ 30
1
vote
9
replies
2.5k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 10 months ago by 68k • written 10 months ago by ▴ 10
0
votes
9
replies
1.9k
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 10 months ago by ▴ 70 • written 11 months ago by • 0
0
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9
replies
16k
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How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2 pvalue visualization enhancedvolcano rnaseq
written 6.2 years ago by • 0
4
votes
9
replies
1.0k
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
2
votes
9
replies
1.2k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
3 months ago Quang NN ▴ 10
4
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9
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1.8k
views
DESeq2 unable to handle large count values
DESeq2
updated 6 months ago by 43k • written 17 months ago by • 0
1
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8
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1.4k
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 9 months ago by 52k • written 10 months ago by • 0
1
vote
8
replies
1.4k
views
DEseq2 time-series design
deseq2
updated 6 months ago by ▴ 10 • written 6.1 years ago by • 0
1
vote
8
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2.5k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
21 days ago • updated 18 days ago ktz • 0
1
vote
8
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936
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
11 months ago boczniak767 ▴ 740
1
vote
8
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2.3k
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
6 weeks ago • updated 16 days ago Luca • 0
0
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8
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4.5k
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DESeq2: handling NA values in colData
deseq2 coldata NA
updated 8 months ago by 43k • written 6.7 years ago by ▴ 170
1
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8
replies
3.9k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 7.1 years ago by ▴ 60
2
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7
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2.2k
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DeSeq2 - Can't fetch any results: Error in .wrap_in_length_one_list_like_object(value, name, x)
deseq2 software error
updated 5 months ago by • 0 • written 5.4 years ago by ▴ 30
3
votes
7
replies
2.1k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 8 weeks ago by ▴ 10 • written 6.1 years ago by ▴ 20
2
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7
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1.5k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
11 months ago sajadahmad41454 • 0
1
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7
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6.7k
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DESeq2 with unbalanced experimental design
deseq2
updated 6 months ago by • 0 • written 10.1 years ago by • 0
4
votes
7
replies
1.8k
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 8 months ago by ▴ 10 • written 9 months ago by ▴ 70
0
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7
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1.1k
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 4 months ago by • 0 • written 4 months ago by • 0
0
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7
replies
859
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DESeq design with and without intercept is giving different results
DESeq2
written 8 months ago by • 0
0
votes
6
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2.0k
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DESeq2 It is correct to use interaction term for patient variability?
deseq2 design interaction term R
written 7.2 years ago by • 0
1
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6
replies
1.9k
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how to analysis htseq-count
deseq2
written 7.3 years ago by ▴ 30
1
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6
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1.3k
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 6 months ago by ★ 4.8k • written 7 months ago by • 0
1
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6
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1.3k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 5 months ago by 43k • written 5 months ago by ▴ 10
0
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6
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1.3k
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
11 months ago Ken C • 0
0
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6
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1.1k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 6 months ago by 43k • written 6 months ago by • 0
3
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6
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30k
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Deseq: What does "BaseMean" mean?
deseq2
written 6.6 years ago by • 0
0
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6
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919
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 11 months ago by ★ 1.4k • written 11 months ago by ▴ 130
3
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6
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3.1k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 10 months ago by ★ 4.8k • written 2.1 years ago by ▴ 20
3
votes
6
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1.0k
views
A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 9 months ago by • 0
3
votes
6
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1.7k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
0
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6
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955
views
Counter-directional LFC shrinkage
DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
2
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6
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1.7k
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 7 weeks ago by • 0 • written 11 months ago by • 0
4
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6
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1.2k
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 28 days ago by ★ 4.8k • written 7 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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