Showing : DEseq2 • reset
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how many significant figures are there in DESeq2 output
DESeq2
updated 11 hours ago by ★ 4.7k • written 1 day ago by ▴ 180
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5
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
4 days ago • updated 3 days ago picasa1983 • 0
3
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7
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1.8k
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 3 days ago by ▴ 10 • written 6.0 years ago by ▴ 20
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264
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How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 5 days ago by 68k • written 5 days ago by • 0
1
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1
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408
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 5 days ago by ★ 1.4k • written 6 days ago by ▴ 10
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1
reply
248
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DEseq2 design for additive treatment
DESeq2
updated 6 days ago by ★ 4.7k • written 7 days ago by • 0
2
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2
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440
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Plot title for PCA in DESeq2
DESeq2
8 days ago • updated 5 days ago AL • 0
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3
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494
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 days ago by 43k • written 12 days ago by • 0
1
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2
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1.0k
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 16 days ago by ★ 4.7k • written 16 days ago by • 0
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1
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137
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 19 days ago by 43k • written 23 days ago by • 0
0
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3
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477
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 19 days ago by • 0 • written 25 days ago by • 0
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2
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352
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 22 days ago by • 0 • written 27 days ago by • 0
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3
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414
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 5 days ago by • 0 • written 27 days ago by • 0
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3
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376
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 27 days ago by • 0 • written 5 weeks ago by ▴ 10
0
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1
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179
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 4 weeks ago by 43k • written 4 weeks ago by • 0
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2
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445
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 4 weeks ago by ★ 1.4k • written 5 weeks ago by • 0
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4
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952
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Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
5 weeks ago • updated 4 weeks ago Quang NN ▴ 10
0
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2
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420
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
5 weeks ago Blandine • 0
0
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5
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330
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 5 weeks ago by • 0
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4
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477
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
5 weeks ago Quang NN ▴ 10
2
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5
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386
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Differential variability modelling with vst() expression
limma DESeq2
written 7 weeks ago by • 0
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3
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533
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 7 weeks ago by • 0
2
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9
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949
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
7 weeks ago • updated 5 weeks ago Quang NN ▴ 10
1
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1
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387
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
0
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1
reply
206
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 7 weeks ago by ★ 1.4k • written 7 weeks ago by • 0
0
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1
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389
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
2
votes
1
reply
387
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
0
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2
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365
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
9 weeks ago • updated 8 weeks ago Kucsera • 0
1
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1
reply
406
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 10 weeks ago by 43k • written 11 weeks ago by • 0
1
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9
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911
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 10 weeks ago by ▴ 30
4
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2
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467
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 10 weeks ago by ★ 4.7k • written 11 weeks ago by ▴ 10
1
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5
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630
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Deseq2 Design
RNASeq DESeq2
updated 10 weeks ago by 68k • written 11 weeks ago by • 0
0
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5
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617
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p value is 0, padj is 0
DESeq2
11 weeks ago Wirayatida • 0
1
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2
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595
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
11 weeks ago georgii.vdovin • 0
0
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7
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928
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 11 weeks ago by • 0 • written 11 weeks ago by • 0
0
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1
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338
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 20
0
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3
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483
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DESeq2 - Comparing Comparisons
DESeq2
updated 11 weeks ago by 68k • written 12 weeks ago by • 0
0
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4
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613
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lfcShrink and alpha value
lfcShrink DESeq2
3 months ago • updated 12 weeks ago cropero • 0
2
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1
reply
369
views
DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 12 weeks ago by 43k • written 3 months ago by • 0
0
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2
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271
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 12 weeks ago by 43k • written 3 months ago by • 0
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2
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305
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
3 months ago Anna • 0
1
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2
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609
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Deseq2 res Function
DESeq2
updated 3 months ago by 68k • written 3 months ago by ▴ 10
0
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4
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499
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
3 months ago NB • 0
0
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5
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530
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Identical samples after deseq2 batch effect removal
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
0
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1
reply
300
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
1
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2
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358
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
3 months ago Denise • 0
0
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1
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209
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eRNAs count
RNASeq DESeq2
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
0
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1
reply
455
views
DESeq2 rerun returns different results
DESeq2
updated 3 months ago by ★ 4.7k • written 3 months ago by • 0
0
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1
reply
317
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 3 months ago by 43k • written 3 months ago by • 0
0
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1
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293
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
Awards • All
Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
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