Showing : DEseq2 • reset
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Should I use the 'log2FoldChange' from lfcShrink() to subset significant DEGs?
lfcshrink DESeq2
written 23 months ago by • 0
2
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1
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752
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 22 months ago by 43k • written 22 months ago by ▴ 20
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3
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LOG2FC DESEQ2
DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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433
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unequal number of treatmets to control
DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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2
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859
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Batch effects removal across mRNA seq studies addressing different biological question: Best approach?
DESeq2
22 months ago Kuldeep • 0
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2
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842
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 22 months ago by 43k • written 22 months ago by • 0
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2
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872
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DESeq2 lfcShrink drastic shrinkage
DESeq2
updated 7 months ago by • 0 • written 22 months ago by • 0
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1.2k
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
22 months ago island • 0
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4
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1.4k
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DESeq2 aborting after upgrade
DESeq2
22 months ago • updated 21 months ago Aarti • 0
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852
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Cross-species analysis using DESeq2 - size factor computation
dese DESeq2
22 months ago pl23 • 0
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3
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1.1k
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Big differences between biological replicates makes DESeq2 result 0
chipseq DifferentialMethylation DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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1.3k
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 22 months ago by • 0
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2
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1.9k
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Regressing out covariates from expression matrix for PCA visualization - can I use coefficients calculated in DESeq2??
DESeq2
22 months ago tombate94 • 0
0
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1
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1.2k
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WGCNA Soft Power
Normalization DESeq2 Network RNASeqData
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
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0
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936
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
22 months ago Jawahar • 0
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2
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829
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Which fasta files to use for tximeta makeLinkTxome
tximeta DESeq2
22 months ago JING • 0
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538
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DESEQ2 reduced model input into Pathfindr
DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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1
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762
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Behavior of most genes in Ribosome-footprints dataset deviates from expected
DESeq2 timecourse time
updated 22 months ago by 43k • written 22 months ago by • 0
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2
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1.0k
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Deleting a column from data frame and then running DESeq2
DESeq2
updated 22 months ago by 43k • written 22 months ago by ▴ 10
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2
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1.8k
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Plotting mean TPM of an expressed gene
DESeq2
22 months ago mp52226 • 0
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869
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Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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1
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603
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[DESEQ2] When to average biological replicates for hierarchical clustering
DESeq2
updated 22 months ago by 68k • written 22 months ago by • 0
2
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2
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625
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How to interpret log2fold values when using numeric contrasts in DESEQ2?
DESeq2
22 months ago pl23 • 0
1
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1
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675
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Looking for a MSigDB chip file
DESeq2
updated 22 months ago by 68k • written 22 months ago by • 0
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1
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1.0k
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DESeq2 multi-factor design and interaction terms
DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
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9
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2.4k
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RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
22 months ago Luca • 0
0
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1
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807
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
22 months ago WS • 0
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3
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2.7k
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DESeq2 design with multiple factors
DESeq2
written 22 months ago by • 0
1
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1
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1.0k
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DESeq2 Normalization for QC Samples
DESeq2 Normalization
updated 22 months ago by 43k • written 22 months ago by • 0
1
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3
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1.2k
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 23 months ago by • 0
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2
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3.6k
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
23 months ago • updated 22 months ago Linton • 0
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5
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1.9k
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Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 22 months ago by ★ 5.0k • written 23 months ago by • 0
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1.0k
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DESeq2 interaction term + sva
sva DESeq2
updated 23 months ago by 43k • written 23 months ago by ▴ 20
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3
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1.2k
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
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967
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
2
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3
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3.6k
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Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 23 months ago by ★ 1.4k • written 23 months ago by • 0
0
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6
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1.5k
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Deseq2 Coefficients from resultsNames() not reflecting all coefficient possibilities.
DESeq2
23 months ago • updated 21 months ago JalapenoCornbread • 0
2
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3
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1.4k
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lfcSE always positive. Does this make sense?
DESeq2
updated 23 months ago by 21k • written 23 months ago by • 0
0
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3
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871
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DESeq2: Difference in DEG numbers when switching reference condition (numerator, denominator) using contrast
DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
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2
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1.7k
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DESeq2 collinearity, adjusting for covariates, and the ground truth
DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
1
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3
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1.1k
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DESeq2: the model matrix is not full rank issue
DESeq2
updated 23 months ago by • 0 • written 23 months ago by • 0
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3
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2.2k
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Difference between vst() and varianceStabilizingTransform()
DESeq2
written 23 months ago by • 0
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5
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1.2k
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Unexpected results for a differential expression analysis between males and females
DESeq2
updated 23 months ago by ★ 3.4k • written 23 months ago by • 0
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5
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2.4k
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scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?
pseudobulk seurat DESeq2
updated 23 months ago by ★ 4.0k • written 23 months ago by • 0
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4
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1.2k
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 22 months ago by 53k • written 23 months ago by • 0
0
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2
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814
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Running DESeq on normalized data
deseq DESeq2
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
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2
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1.2k
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Linear Model Fitting and Colinearity
dese DESeq2
23 months ago Hugo • 0
2
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1
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634
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removeBatchEffect with non-linear model fit
limma DESeq2
updated 23 months ago by 53k • written 23 months ago by • 0
1
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13
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2.4k
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Small RNA-seq Analysis DESEQ2 : Unexpected Significance
conditions replicates SmallRNAData DESeq2
updated 22 months ago by ★ 4.0k • written 23 months ago by ▴ 10
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1
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1.7k
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Interaction terms in DESeq2
RNASeqData RnaSeqSampleSize DESeq2
updated 23 months ago by 68k • written 23 months ago by • 0
4,839 results • Page 8 of 97
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Replies
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
Answer: Large logFC but somewhat high FDR by Gordon Smyth 53k
Glad you're getting good use out of the package. The results that you show seem pretty much as one would expect, with nothing surprising. …
Comment: After running samtools, the featureCounts command crashed. by MarcHintz99 • 0
Thanks for shairng https://subread.sourceforge.net/
Votes
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
A: p.adjust BH generates duplicate values
Answer: gene Set with high AUC score but no cells assigned to cell type
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