Showing : deseq2 • reset
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Deseq2 Design
RNASeq DESeq2
updated 13 months ago by 68k • written 13 months ago by • 0
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p value is 0, padj is 0
DESeq2
13 months ago Wirayatida • 0
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
13 months ago georgii.vdovin • 0
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 13 months ago by • 0 • written 13 months ago by • 0
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585
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 13 months ago by 43k • written 13 months ago by ▴ 20
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3
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DESeq2 - Comparing Comparisons
DESeq2
updated 13 months ago by 68k • written 13 months ago by • 0
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lfcShrink and alpha value
lfcShrink DESeq2
13 months ago anon • 0
2
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1
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808
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 13 months ago by 43k • written 13 months ago by • 0
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540
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
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524
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
13 months ago Anna • 0
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840
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Deseq2 res Function
DESeq2
updated 13 months ago by 68k • written 14 months ago by ▴ 10
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799
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
14 months ago NB • 0
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5
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802
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Identical samples after deseq2 batch effect removal
DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
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618
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 14 months ago by 68k • written 14 months ago by • 0
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523
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
14 months ago Denise • 0
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464
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eRNAs count
RNASeq DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
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651
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DESeq2 rerun returns different results
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
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565
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 14 months ago by 43k • written 14 months ago by • 0
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1
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680
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
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2
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1.1k
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Handling biological replicates in DESeq2
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
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3
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 7.0 years ago by ▴ 30
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 14 months ago by 43k • written 14 months ago by ▴ 10
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 14 months ago by • 0
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
14 months ago LuciaNhu • 0
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Average expression of genes across replicates
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
14 months ago info ▴ 10
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Question about using LRT test for time course experiments with DESeq2
DESeq2
updated 9 months ago by • 0 • written 14 months ago by • 0
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580
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Deseq to output continous sequencing data
DESeq2
updated 14 months ago by 43k • written 15 months ago by • 0
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4
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1.4k
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Adjusted p-values become NA when sub-setting samples
DESeq2
15 months ago • updated 14 months ago txema.heredia • 0
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1.6k
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 14 months ago by • 0
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2
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924
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 15 months ago by • 0
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511
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
2
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3
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1.3k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
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DESeq2 - interactions when using factors concatenated into group
DESeq2
15 months ago • updated 14 months ago boczniak767 ▴ 740
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402
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
15 months ago JY • 0
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495
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
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533
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how to extract expression matrix post deseq2
DESeq2
written 15 months ago by • 0
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2
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568
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Using Normalized Counts in DESeq2
DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
3
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659
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When running contrasts, does it use normalized read counts?
DESeq2
15 months ago Katherine ▴ 20
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1
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445
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 15 months ago by ★ 1.4k • written 15 months ago by • 0
3
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4
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1.4k
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
15 months ago Eva ▴ 10
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4
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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562
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
2
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4
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999
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
15 months ago jihoon.kim.1495 ▴ 10
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1.5k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 14 months ago by 43k • written 15 months ago by • 0
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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2
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750
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
15 months ago paul.meraner • 0
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0
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648
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
15 months ago • updated 14 months ago info ▴ 10
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1.5k
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heatmap with batch effect
DESeq2 BatchEffect
written 15 months ago by • 0
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2
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802
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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 15 months ago by 43k • written 15 months ago by • 0
4,844 results • Page 3 of 97
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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