Showing : differential gene expression • reset
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Why DESeq2 and edgeR give different results?
deseq2 rnaseq differential gene expression edger
updated 4.5 years ago by 53k • written 7.5 years ago by ▴ 120
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4
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edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 7.6 years ago by 53k • written 7.6 years ago by • 0
5
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12
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Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 7.6 years ago by 53k • written 7.6 years ago by ▴ 120
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3
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TPM data Differential expression analysis
edger limma differential gene expression
updated 3.6 years ago by 53k • written 7.6 years ago by • 0
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3
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950
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Differentially expressed genes detection between three classes with a batch effect in DESeq2
deseq2 batch effect differential gene expression
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
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1
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1.5k
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Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 7.6 years ago by ★ 29k • written 7.6 years ago by • 0
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4
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Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 7.6 years ago by ▴ 280 • written 7.6 years ago by ▴ 40
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Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
edger differential gene expression upregulated genes downregulated genes
updated 7.7 years ago by • 0 • written 7.7 years ago by ▴ 60
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Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
7.7 years ago David R ▴ 90
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DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
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2
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3.9k
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Going crazy with normalizing TCGA raw rsem gene count
cancer tcga normalization rnaseq differential gene expression
updated 7.7 years ago by • 0 • written 10.6 years ago by • 0
2
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0
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Job: PhD Studentship - Investigating Regulation of Transcription and Translation in Prostate Cancer
mirna riboseq smallrna differential gene expression Job
7.7 years ago Andy Lynch ▴ 120
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4
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Upregulation and Downregulation of Gene Ontology terms
microarray david differential gene expression GO
7.7 years ago seendey16 • 0
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1
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1.6k
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Differential Coexpression Analysis
differential analysis differential gene expression coexpression correlation
updated 7.8 years ago by ★ 3.0k • written 7.8 years ago by ▴ 20
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3
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edgeR multifactorial analysis implementation with RNA-Seq data
edger multifactorial design multiple comparisons differential gene expression
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 840
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0
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677
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plotMA is not centered around zero for logFC
microarray differential gene expression
7.8 years ago twentestat • 0
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3
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1.8k
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Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
7.8 years ago cherlyn.t • 0
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8
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6.6k
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Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
7.8 years ago Marina ▴ 40
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1
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1.3k
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Requesting help with RNA-Seq differential gene analysis
differential gene expression gene expression clustering gene regulatory network normalization
7.8 years ago sagnik • 0
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2
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4.5k
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DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2 goseq rnaseq go enrichment differential gene expression
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
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Performing differential gene analysis on RT PCR experimental data
differential gene expression
updated 7.8 years ago by 53k • written 7.9 years ago by ▴ 10
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4
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Pairwise Comparison between A Large Number of Groups
deseq2 differential gene expression
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
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1
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3.7k
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DESeq2 design model/contrasts question 3 level condition
deseq2 model design differential gene expression experimental design
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
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2
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Differential expression of RNA seq data at gene level (for Beginner)
deseq2 differential gene expression bioconductor
updated 7.9 years ago by ▴ 130 • written 7.9 years ago by • 0
2
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3
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2.0k
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Can DESeq2/edgeR perform differential analysis for rRNA?
deseq2 edger rRNA differential gene expression
8.0 years ago r.aprianto ▴ 30
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RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 10
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What package should I use to retrieve chromosome location for Affymetrix id of gene symbol id while doing gene expression microarray analysis ?
affymetrix microarrays differential gene expression
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 20
3
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Applying replaceOutliers rather than throwing out genes when model includes continuous variable
deseq2 rnaseq differential gene expression differential expression
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
2
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9
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Loads, really loads of DEGs after edgeR differential analysis
rnaseq edger normalization differential gene expression
8.0 years ago David R ▴ 90
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5
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Constant High Padj Values
deseq2 differential gene expression multiple factor design padj
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
2
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9
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SNP-level Allele-specific expression detection using DESeq2 in an unpaired experimental design
deseq2 rnaseq differential gene expression
8.1 years ago • updated 8.0 years ago engelbrecht.stephan ▴ 10
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Differential expression between multiple groups
multiple groups differential gene expression microarray
8.0 years ago A ▴ 60
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7
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5.4k
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deseq2 analysis with multiple factors and interaction terms
deseq2 multiple factor design differential analysis differential gene expression
updated 8.1 years ago by 43k • written 8.1 years ago by ▴ 10
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4
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limma. After running a differential expression analysis... Can you get the individual gene expression levels between individual contrasts for each of…
limma gene expression differential gene expression
8.1 years ago arfranco ▴ 130
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4
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Multiple differential expression analyses with DESeq2
deseq2 differential gene expression
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
1
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Strange distribution of logFC
edger deseq2 rnaseq differential gene expression
updated 8.1 years ago by ★ 29k • written 8.1 years ago by ▴ 20
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Ballgown with replicates and the adjustvars option
ballgown rnaseq differential gene expression
updated 8.1 years ago by ▴ 210 • written 8.3 years ago by • 0
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Design model for DESeq2 analysis
deseq2 differential gene expression
updated 8.1 years ago by ▴ 690 • written 8.1 years ago by ▴ 20
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3
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1.6k
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Adding gene names which are differentially expressed in the plot
edgeR plot differential gene expression
8.1 years ago fawazfebin ▴ 60
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3
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2.3k
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Differential Expression analysis between distinct scRNA-seq datasets
scrna scrnaseq differential gene expression
updated 8.1 years ago by ▴ 980 • written 8.1 years ago by • 0
0
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3
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replicates and groups of samples: what's the right DESeq2 model?
deseq2 rnaseq differential gene expression
updated 8.1 years ago by ▴ 690 • written 8.1 years ago by • 0
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0
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829
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comparison of expression between orthologous species
rnaseq differential gene expression
8.2 years ago laksharikrish • 0
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5
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Differential gene expression: common changes in response to treatment across cell types
deseq2 differential gene expression
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by ▴ 10
3
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6
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2.9k
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Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix toptable makecontrasts differential gene expression
8.2 years ago stinehedensted • 0
0
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3
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1.8k
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Differential expression of individual genes using edgeR
edger differential gene expression
8.2 years ago fawazfebin ▴ 60
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2
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1.6k
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Differential gene expression for multi-factorial experiment using edgeR
edger differential gene expression multiple factor design
updated 8.2 years ago by ★ 29k • written 8.2 years ago by • 0
0
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5
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Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
8.2 years ago lirongrossmann ▴ 80
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19
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5.2k
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Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by ▴ 50
2
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3
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Differential expression of nomalised and log2 transformed data in limma
limma lmfit model.matrix differential gene expression
8.2 years ago stinehedensted • 0
0
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1
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2.1k
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DESeq2 biological replicates and RIN values
deseq2 differential gene expression covariates rnaseq
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
272 results • Page 2 of 6
Recent ...
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
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…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
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