Showing : DifferentialExpression • reset
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DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 2.1 years ago by • 0 • written 2.7 years ago by • 0
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2
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6.7k
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Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 2.6 years ago by ★ 4.0k • written 2.6 years ago by ▴ 10
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DESeq2: removing levels from a factor or not having them in the analysis at all
deseq2 differentialexpression
updated 9.6 years ago by 41k • written 9.6 years ago by ▴ 90
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13
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6.4k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 11 weeks ago by ★ 4.0k • written 2.1 years ago by ▴ 30
3
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5
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How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
2.6 years ago zhxiaokang ▴ 20
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4.1k
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Manually calculating log2 fold change values from DESeq2 normalized counts
DESeq2 DifferentialExpression
16 months ago Jayesh Kumar • 0
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8
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3.3k
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 24 months ago by ▴ 10
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Comparisons both between and within subjects using DESeq2
deseq2 edger differentialexpression
9.5 years ago asaferali • 0
2
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2.9k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
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7
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2.3k
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topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 3.5 years ago by 50k • written 3.5 years ago by ▴ 20
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2.2k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 20 months ago by 50k • written 2.7 years ago by ▴ 10
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6
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2.2k
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Repeated measures per individual and unbalanced number of measures per individual: DE between groups still an ordinary two-group comparison?
differentialexpression deseq2 limma edger repeatedmeasures
4.6 years ago • updated 2.3 years ago hermidalc ▴ 20
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2.1k
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Limma interaction term
RNASeqData limma DifferentialExpression
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
2
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8
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2.0k
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
2.9 years ago Jane ▴ 10
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2.0k
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
2.5 years ago p.l.chen • 0
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2
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1.9k
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Normal Patient Samples from GSE62944
GSE62944 annotationhub differentialexpression
updated 8.1 years ago by ▴ 390 • written 8.1 years ago by • 0
1
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2
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1.8k
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unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.0 years ago Ismail • 0
0
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2
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1.7k
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Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 2.2 years ago by 50k • written 2.2 years ago by • 0
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1
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1.7k
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TCC::ERROR: Need the design matrix for GLM.
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 10.0 years ago by ▴ 10 • written 10.0 years ago by ▴ 100
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1.7k
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Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 14 months ago by ★ 4.0k • written 14 months ago by ▴ 10
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8
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1.7k
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DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
2.3 years ago dadca596 • 0
4
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5
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1.7k
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What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 24 months ago by • 0 • written 2.2 years ago by ▴ 30
2
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2
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1.6k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
2.9 years ago SUMIT • 0
0
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1
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1.6k
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TCC::ERROR: Need the design matrix for GLM
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 10.0 years ago by ▴ 10 • written 10.0 years ago by 50k
5
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6
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1.6k
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DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
0
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5
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1.6k
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Weird output of DESeq2 when using single sample from one group agains the other group (6 samples), really need some help
DifferentialExpression DESeq2
updated 2.3 years ago by 41k • written 2.3 years ago by ▴ 10
6
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3
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1.6k
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differential gene expression
limma differentialexpression
updated 9.6 years ago by ▴ 760 • written 9.6 years ago by ▴ 20
1
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8
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1.6k
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edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
22 months ago giBio • 0
5
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9
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1.6k
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Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 2.7 years ago by 65k • written 2.8 years ago by ▴ 830
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7
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1.5k
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How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 17 months ago by 50k • written 18 months ago by • 0
2
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3
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1.5k
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Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
1
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8
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1.5k
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Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 10 months ago by • 0
0
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8
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1.4k
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Three conditions and two time points
DifferentialExpression DESeq2 time
2.6 years ago • updated 2.5 years ago AZ ▴ 30
0
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2
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1.4k
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How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
3.4 years ago harelarik ▴ 60
0
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7
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1.4k
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DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 2.0 years ago by 41k • written 2.1 years ago by • 0
3
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7
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1.4k
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Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 3.2 years ago by 50k • written 3.2 years ago by ▴ 30
3
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6
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1.4k
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One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 17 months ago by • 0
2
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3
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1.4k
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DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
0
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3
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1.4k
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Offsets and normalization in EdgeR
edgeR DifferentialExpression
updated 3.5 years ago by 50k • written 3.5 years ago by • 0
6
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11
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1.4k
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
14 months ago mohammedtoufiq91 ▴ 10
2
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2
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1.3k
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Why does limma want log2 intensities but DESeq2 use raw counts?
limma DifferentialExpression DESeq2
3.0 years ago • updated 2.9 years ago tjbencomo • 0
3
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4
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1.3k
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How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
2.0 years ago mohammedtoufiq91 ▴ 10
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10
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1.3k
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Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
3.5 years ago Hajar • 0
0
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8
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1.3k
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Swish log2FC NA output
swish fishpond DifferentialExpression
21 months ago jvandinter • 0
3
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6
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1.3k
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Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 50
3
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6
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1.3k
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do I have to do this step in creating DGEList ?
DifferentialExpression
updated 14 months ago by 50k • written 14 months ago by • 0
0
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7
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1.2k
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Help with differential gene expression using Agilent Microarray data (from GEO database)
limma Paireddata DifferentialExpression
updated 17 months ago by 65k • written 18 months ago by • 0
0
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5
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1.2k
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DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 19 months ago by 41k • written 2.7 years ago by • 0
0
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1
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1.2k
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read.maimages problem under sun ?
Microarray OneChannel TwoChannel DifferentialExpression Preprocessing QualityControl affy
17.0 years ago Amin Moghaddasi ▴ 130
0
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2
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1.2k
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Comparison when Control is in differen batch
DESeq2 DifferentialExpression
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by ▴ 30
50 results • Page 1 of 1
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Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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