Showing : DeSeq2 • reset
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 16 months ago by 43k • written 17 months ago by • 0
0
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1
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638
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unreal negative log2fc values
DESeq2 des
updated 17 months ago by 68k • written 17 months ago by • 0
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1
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557
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LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
1
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8
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1.9k
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 17 months ago by 53k • written 17 months ago by • 0
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2
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3.2k
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Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
17 months ago sropri • 0
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1
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566
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 17 months ago by 68k • written 17 months ago by • 0
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1
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771
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DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
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5
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1.1k
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DESeq2 ML Query
DESeq2
updated 16 months ago by 43k • written 17 months ago by • 0
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3
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1.0k
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Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
17 months ago • updated 16 months ago David W. H. • 0
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1
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722
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 17 months ago by 68k • written 17 months ago by • 0
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3
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1.9k
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
17 months ago Tanvi • 0
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1
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1.3k
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In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
DESeq2
updated 17 months ago by 43k • written 18 months ago by • 0
2
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1
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678
views
Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 17 months ago by 43k • written 18 months ago by ▴ 10
2
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1
reply
820
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by ▴ 70
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9
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3.2k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 17 months ago by 68k • written 17 months ago by ▴ 10
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3
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1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 17 months ago by 68k • written 17 months ago by ▴ 50
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6
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3.5k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 17 months ago by ★ 5.0k • written 2.7 years ago by ▴ 20
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2
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936
views
Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
18 months ago • updated 17 months ago BioinfGuru ▴ 70
1
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2
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1.3k
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Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
18 months ago a_p • 0
0
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1
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726
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
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1
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642
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
1
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2
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2.8k
views
using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 18 months ago by ▴ 40 • written 6.1 years ago by • 0
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1
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524
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multiple condition issue running DESeq
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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3
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747
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Ploting of normalized counts after batch removal
DESeq2
updated 18 months ago by 53k • written 18 months ago by ▴ 10
1
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1
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496
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makeExampleDESeqDataSet using pilot data
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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2
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672
views
Best way to describe DEseq2 design
DESeq2
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
1
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2
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824
views
Deseq2
DESeq2 rnaseqGene
updated 18 months ago by ▴ 220 • written 18 months ago by • 0
1
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1
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573
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 18 months ago by 68k • written 18 months ago by ▴ 740
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6
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1.2k
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Counter-directional LFC shrinkage
DESeq2
updated 18 months ago by 43k • written 18 months ago by • 0
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2
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1.2k
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
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3
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2.0k
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GSVA function
DESeq2 GSVA ssGSEA
updated 18 months ago by ★ 3.4k • written 18 months ago by • 0
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2
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974
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
18 months ago sukeshinik5 ▴ 20
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4
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2.2k
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
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8
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1.3k
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
18 months ago boczniak767 ▴ 740
1
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3
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1.0k
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 18 months ago by 68k • written 18 months ago by ▴ 740
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6
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1.6k
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
18 months ago Ken C • 0
2
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4
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1.1k
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 18 months ago by 43k • written 18 months ago by • 0
4
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9
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1.4k
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
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3
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787
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 18 months ago by 43k • written 18 months ago by • 0
0
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1
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765
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 18 months ago by 43k • written 18 months ago by • 0
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9
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2.3k
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 18 months ago by ▴ 70 • written 18 months ago by • 0
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2
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1.1k
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
18 months ago BioinfGuru ▴ 70
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1
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627
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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1
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721
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
2
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7
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2.0k
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
19 months ago sajadahmad41454 • 0
2
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1
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836
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Handling multiple differential expression comparisons
DESeq2
19 months ago • updated 17 months ago Zainab ▴ 20
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6
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1.2k
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 19 months ago by ★ 1.4k • written 19 months ago by ▴ 130
2
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6
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2.3k
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 9 months ago by • 0 • written 19 months ago by • 0
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2
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526
views
DESeq2 v1.35.0
DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
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2
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904
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Deseq2 and Normalization of RNA sequencing data
DESeq2
19 months ago kcarey • 0
4,840 results • Page 5 of 97
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Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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