Showing : DIfferential expression • reset
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How to perform time-course differential expression with "erroneous" baseline in edgeR?
edger differential expression timecourse
updated 7.6 years ago by 53k • written 7.6 years ago by • 0
2
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1
reply
5.4k
views
Using DESeq2 to analyse TCGA data
deseq2 tcga tcgabiolinks gene expression differential expression
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
1
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3
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1.9k
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Differential expressiong with two groups in BASiCS
BASiCS single-cell bayesian differential expression
updated 7.6 years ago by ▴ 10 • written 7.6 years ago by ▴ 10
0
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2
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1.4k
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Run tweeDEseq on Flux-capacitor RPKM values
tweedeseq differential expression
updated 7.6 years ago by ★ 3.4k • written 7.6 years ago by • 0
0
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2
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1.2k
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DESeq2, no significantly DE genes
deseq2 differential expression adjusted pvalue
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 60
0
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0
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816
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TCGAvisualize_EAbarplot error in TCGAbiolinks
tcgabiolinks tcgavisualize_EAbarplot differential expression
7.7 years ago fawazfebin ▴ 60
1
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5
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8.3k
views
DESeq2 and edgeR getting very different results
edger deseq2 differential expression
updated 7.7 years ago by ▴ 20 • written 7.7 years ago by • 0
2
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2
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1.5k
views
How to add more columns to ReportingTools output?
reportingtools microarray annotation differential expression differential analysis
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
3
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1
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1.4k
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Applying replaceOutliers rather than throwing out genes when model includes continuous variable
deseq2 rnaseq differential gene expression differential expression
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
1
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6
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4.1k
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Two-way anova 2x2 design with limma
limma microarray differential expression
7.8 years ago damoros • 0
2
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8
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1.9k
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Deseq2 result for a variable
deseq2 differential expression results
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
1
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3
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1.6k
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DESeq: large difference in number of replicates per condition
deseq2 rnaseq differential expression
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
5
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4
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1.8k
views
Differential expression analysis desgin
differential expression deseq2 edger interactions limma
updated 7.9 years ago by 53k • written 7.9 years ago by ▴ 10
0
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0
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1.3k
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How to specify covariates in maSigPro analysis (like limma)
masigpro covariates limma differential expression time-course
7.9 years ago veersingh.marwah • 0
3
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4
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5.8k
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About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
8.0 years ago David Requena ▴ 20
2
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8
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3.2k
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Limma for differential expression in a time-course
limma multiple time points time-course differential expression
updated 8.0 years ago by ★ 29k • written 8.0 years ago by • 0
0
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2
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1.4k
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limma voom for single factor
limma voom differential expression
updated 8.0 years ago by 53k • written 8.0 years ago by • 0
0
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1
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1.1k
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Read normalization in a complex sample
deseq2 differential expression normalization
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
2
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1
reply
1.3k
views
Derinder options (species, annotations style)
derfinder rnaseq differential expression
updated 8.1 years ago by ★ 1.1k • written 8.1 years ago by ▴ 20
1
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2
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2.7k
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How to adjust for different cell type mixtures in differential expression analysis?
cell types differential expression adjustment mixtures rnaseq
updated 8.2 years ago by ★ 7.9k • written 8.2 years ago by ▴ 90
1
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2
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1.7k
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accounting for phylogenetic non-independence in differential expression analysis
edger differential expression phylogenetic comparative methods
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
1
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1
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988
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Differential expression after different normalization methods
deseq2 differential expression
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
1
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2
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5.0k
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Multiple comparisons for DE analysis with DESeq2
deseq2 mirna-seq experimental design differential expression
updated 8.3 years ago by ▴ 690 • written 8.3 years ago by ▴ 10
3
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5
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7.9k
views
Ballgown up and down regulated genes
ballgown differential expression
updated 8.4 years ago by • 0 • written 9.6 years ago by ▴ 10
2
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2
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2.8k
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Pairwise differential expression analysis with batch effect using edgeR and SVA
edger rna-seq sva differential expression
updated 8.4 years ago by ★ 29k • written 8.4 years ago by • 0
2
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0
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858
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differential expression with heterogenous disease
heterogenous differential expression individual effects
8.4 years ago aec ▴ 90
2
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3
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3.1k
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How to deal with up to 75% of DE genes in RNA-seq (TMM, edgeR) ?
differential expression TMM normalization rnaseq edger
8.4 years ago aec ▴ 90
1
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2
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2.4k
views
How to proceed with different degradation levels of RNA-seq samples?
degradation RNA-seq variability differential expression brain
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 90
1
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3
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1.8k
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How different ploidy affect differential expression analysis with RNA-seq
ploidy normalization rna-seq differential expression assumption
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 90
0
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0
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1.5k
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Please help with ballgown problem
ballgown differential expression
8.5 years ago Sara ▴ 20
2
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5
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1.8k
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Comparing across sets of regulated genes -- Strategies?
limma differential expression
updated 8.6 years ago by ▴ 760 • written 8.6 years ago by ▴ 30
6
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4
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2.8k
views
Alternate expression of splice isoforms on Affy Clariom D assay
alternate expression differential expression affy
updated 8.6 years ago by 68k • written 8.6 years ago by ▴ 20
2
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9
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2.8k
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Limma: Defining the design matrix of a linear mixed model
rnaseq limma differential expression
8.6 years ago j.baldauf • 0
2
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3
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3.6k
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Analysis of RNA-seq time series with edgeR
edger rna-seq differential expression timecourse time course
updated 8.9 years ago by ★ 29k • written 8.9 years ago by • 0
1
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2
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1.4k
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2-Factor Experiment in edgeR, Effect of no reps in one set and two reps in others
rnaseq edger differential expression dispersion
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by • 0
1
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5
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1.3k
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differential expression analysis in edgeR when you have 2 experiments and batch effect in 1 of the 2 experiments.
edger batch effect differential expression
8.9 years ago sezimmer • 0
1
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1
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1.7k
views
expression profiles between DESeq2 and Mfuzz
deseq2 mfuzz differential expression timecourse
updated 8.9 years ago by 43k • written 8.9 years ago by ★ 1.5k
3
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1
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2.0k
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Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 9.0 years ago by ★ 29k • written 9.0 years ago by • 0
4
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6
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3.0k
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Find if a covariate has effect on gene expression level using edgeR and DESeq2
edger deseq2 model matrix differential expression
9.0 years ago ta65 • 0
5
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3
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3.8k
views
Error when calculating DE using the classical approach in edgeR
edgeR differential expression rna-seq
updated 9.0 years ago by 53k • written 9.0 years ago by • 0
0
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0
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1.5k
views
SCDE for differential expression
scde differential expression single cell
9.1 years ago mnaymik ▴ 10
2
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2
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2.3k
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Analysis of shRNA screen data
shrna edger deseq2 differential expression normalized counts
9.1 years ago Jane Merlevede ▴ 90
3
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5
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2.4k
views
DESeq2: Appropriate way to deal with knockouts in experiment design (RIPSeq)
deseq2 differential expression immunoprecipitation
updated 9.1 years ago by 43k • written 9.1 years ago by ▴ 40
2
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1
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1.2k
views
edgeR - testing interaction in a scenario of 2 tissues and 2 ages
edgeR R differential gene expression differential expression
updated 9.2 years ago by ★ 29k • written 9.2 years ago by • 0
3
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6
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1.9k
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Question about edgeR usage with one case and multiple controls
edgeR differential expression without replicate
9.2 years ago gavin.oliver • 0
3
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10
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5.4k
views
Differential expression analysis of already normalized sequence counts
differential expression normalization deseq2
updated 9.2 years ago by 43k • written 9.2 years ago by ▴ 20
1
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1
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1.9k
views
Differential binding using csaw
csaw differential binding analysis chipseq differential expression differential gene expression
updated 9.4 years ago by ★ 29k • written 9.4 years ago by ▴ 10
4
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2
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4.1k
views
DESeq2/SAMSeq - analysing subset of genes from RNASeq dataset
deseq2 SAMseq differential expression
updated 9.5 years ago by 43k • written 9.5 years ago by • 0
8
votes
3
replies
19k
views
edgeR normalization method
edgeR differential expression normalization
updated 9.5 years ago by ★ 29k • written 9.5 years ago by ▴ 20
5
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3
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4.9k
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edgeR - how to convert DGELRT and other classes to .csv files
edgeR differential expression file conversion
updated 3.3 years ago by • 0 • written 9.5 years ago by ▴ 10
131 results • Page 2 of 3
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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …
Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k
> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values by Lina ▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
Votes
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
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