Showing : desEQ2 • reset
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p value is 0, padj is 0
DESeq2
13 months ago Wirayatida • 0
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2
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1.2k
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
13 months ago georgii.vdovin • 0
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7
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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
0
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1
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583
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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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813
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DESeq2 - Comparing Comparisons
DESeq2
updated 13 months ago by 68k • written 13 months ago by • 0
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4
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1.0k
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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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801
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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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2
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539
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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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2
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517
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
13 months ago Anna • 0
1
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2
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834
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Deseq2 res Function
DESeq2
updated 13 months ago by 68k • written 13 months ago by ▴ 10
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4
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798
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
13 months ago NB • 0
0
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5
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801
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Identical samples after deseq2 batch effect removal
DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
0
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1
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616
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 13 months ago by 68k • written 13 months ago by • 0
1
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2
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522
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
14 months ago • updated 13 months ago Denise • 0
0
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1
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463
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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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1
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650
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DESeq2 rerun returns different results
DESeq2
updated 14 months ago by ★ 5.0k • written 14 months ago by • 0
0
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1
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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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676
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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
2
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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
5
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3
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29k
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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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6
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1.7k
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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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2
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594
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 14 months ago by • 0
4
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5
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
14 months ago LuciaNhu • 0
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1
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785
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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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0
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457
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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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11
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2.6k
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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
0
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1
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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
1
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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
3
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3
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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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920
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 14 months ago by • 0
0
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1
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510
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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
1
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4
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1.2k
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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
0
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1
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494
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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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2
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529
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how to extract expression matrix post deseq2
DESeq2
written 15 months ago by • 0
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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2
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657
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When running contrasts, does it use normalized read counts?
DESeq2
15 months ago Katherine ▴ 20
0
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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
1
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4
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1.4k
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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
0
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1
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561
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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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992
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
15 months ago jihoon.kim.1495 ▴ 10
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6
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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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749
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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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646
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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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6
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1.5k
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heatmap with batch effect
DESeq2 BatchEffect
written 15 months ago by • 0
0
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2
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799
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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
1
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1
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1.2k
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 15 months ago by 68k • written 15 months ago by • 0
4,843 results • Page 3 of 97
Recent ...
Replies
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Votes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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