Showing : deseq2 • reset
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 15 months ago by 68k • written 15 months ago by • 0
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1
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743
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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616
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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2
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948
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Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 15 months ago by 43k • written 16 months ago by ▴ 10
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2
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DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 15 months ago by 43k • written 16 months ago by • 0
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DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2 Bioconductor
updated 15 months ago by 43k • written 16 months ago by ▴ 10
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6
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 15 months ago by ★ 5.0k • written 16 months ago by • 0
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492
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Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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9
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8.5k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 16 months ago by 68k • written 9.6 years ago by ▴ 10
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647
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Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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2
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873
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PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
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5
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2.4k
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DESeq2 Multi-factor design not full rank
RNASeq DESeq2
written 4.7 years ago by • 0
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6
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2.0k
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[DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Application
DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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6
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32k
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Deseq: What does "BaseMean" mean?
deseq2
written 7.3 years ago by • 0
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2
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1.7k
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Understanding Contrasts and Interaction in DESeq2 for 2 genotypes, 2 treatments
RNASeq DESeq2
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
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11
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1.8k
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Size factor normalized counts for between sample comparisons - correct?
DESeq2
16 months ago boczniak767 ▴ 740
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4
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880
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Gene filtering in DESeq2
DESeq2
updated 16 months ago by ★ 5.0k • written 16 months ago by • 0
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2
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869
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Inquiry on Using DESeq2 for Analyzing Differential Translation Efficiency
RiboSeq DESeq2
written 16 months ago by • 0
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2
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522
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Deseq2 - differenc in results
DESeq2
written 16 months ago by • 0
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1.1k
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DESeq design with and without intercept is giving different results
DESeq2
written 17 months ago by • 0
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5
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1.6k
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 17 months ago by 53k • written 17 months ago by • 0
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3
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1.2k
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More significant genes after lfcShrink in DEseq2?
DESeq2
written 17 months ago by • 0
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3
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1.0k
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 17 months ago by 53k • written 17 months ago by • 0
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2
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717
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Analysis of transcription inhibition with DESeq2
SpikeIn DESeq2 Normalization
written 17 months ago by • 0
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5
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4.6k
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 12 months ago by ▴ 20 • written 17 months ago by • 0
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3
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1.8k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
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2
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1.3k
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R is Removing the Gene Names in My Count Data
DESeq2
updated 17 months ago by ▴ 70 • written 17 months ago by • 0
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4
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1.6k
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Recommendations for DESeq2 Independent Filtering with Pseudobulk Data
DESeq2 independentfiltering glmGamPoi
17 months ago • updated 16 months ago Bob ▴ 30
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650
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Using DESeq2 for Analyzing AMR Gene Variations in Water Samples Post-Treatment
DESeq2 NanoporeRNASeq DNASeq
updated 17 months ago by 43k • written 17 months ago by • 0
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3
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1.2k
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 17 months ago by • 0
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5
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2.5k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
2
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1.8k
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DESeq2 is it OK to scale transformed data in order to plot heatmaps?
DESeq2 heatmaps
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
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2
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929
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Why is the inclusion of RUVs not reflected in the EDA plots produced from normalised counts extracted from deseq2?
RUVSeq DESeq2 dese
17 months ago BioinfGuru ▴ 70
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830
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Combining DESeq2 and Within-Group Variability to Identify Stochastic Genes
DESeq2
17 months ago DL • 0
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3
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961
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RNA-seq with DESeq2 shrinkage estimation
Regression DESeq2 rnaseqGene
updated 17 months ago by 68k • written 17 months ago by • 0
6
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15
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2.7k
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Deseq2 design formula and analysis with internal controls
DESeq2
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
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2
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1.4k
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How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2 tximport
17 months ago grothmn • 0
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1.3k
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HELP - DESeq2 difference between LRT and Wald Test in RNA-seq/ATAC-seq
DESeq2 LRT Wald
updated 17 months ago by 68k • written 17 months ago by • 0
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7
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2.5k
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
updated 17 months ago by ▴ 10 • written 18 months ago by ▴ 70
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913
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DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
updated 17 months ago by 43k • written 18 months ago by • 0
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1.0k
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
updated 17 months ago by 43k • written 18 months ago by • 0
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1.1k
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Comparing one group against multiple groups in DESeq2
DESeq2
written 24 months ago by • 0
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3
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3.2k
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Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
written 18 months ago by • 0
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6
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1.4k
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
written 18 months ago by • 0
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3
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DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
written 18 months ago by ▴ 10
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3
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1.0k
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
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3
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969
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Doubt about model in paired samples (intercept ?)
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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10
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2.2k
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Two treatments, one control
DESeq2 stageR
18 months ago alephreish • 0
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2.1k
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How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
18 months ago Fiona • 0
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1.0k
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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 18 months ago by • 0
4,844 results • Page 4 of 97
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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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