Showing : DifferentialExpression • reset
2
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
0
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4
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743
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
2
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3
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919
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Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
2.2 years ago nhaus ▴ 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
3
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8
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3.4k
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.0 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
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
1
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2
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421
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
0
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2
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282
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 7 weeks ago by 50k • written 7 weeks ago by • 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 2.8 years ago by 65k • written 2.8 years ago by ▴ 830
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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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7
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1.2k
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Which Limma guide is recommended ?
limma R DifferentialExpression
2.1 years ago • updated 2.0 years ago JAcky • 0
4
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10
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1.4k
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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
1
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3
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407
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
2
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6
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776
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
1
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3
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598
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
3
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5
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4.8k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
2.7 years ago zhxiaokang ▴ 20
9
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13
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6.5k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 3 months ago by ★ 4.1k • written 2.1 years ago by ▴ 30
2
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8
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2.1k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.0 years ago • updated 2.9 years ago Jane ▴ 10
1
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2
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1.1k
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Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 3.5 years ago by 41k • written 3.5 years ago by • 0
0
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3
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2.9k
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Comparisons both between and within subjects using DESeq2
deseq2 edger differentialexpression
9.5 years ago asaferali • 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 10.1 years ago by ▴ 10 • written 10.1 years ago by 50k
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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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
3
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7
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1.4k
views
Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 3.2 years ago by 50k • written 3.2 years ago by ▴ 30
0
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1
reply
676
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Wald or LR Test
DESeq2 DifferentialExpression
updated 3.1 years ago by 41k • written 3.1 years ago by • 0
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
5
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2
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2.2k
views
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
0
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3
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858
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Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 16 months ago by 41k • written 16 months ago by • 0
5
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3
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712
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 50
4
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3
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1.2k
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Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 2.3 years ago by 65k • written 2.3 years 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 20 months ago by 41k • written 2.7 years ago by • 0
1
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2
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663
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DESeq2 with very large feature set
DESeq2 DifferentialExpression
3.5 years ago ramiro.barrantes ▴ 10
4
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2
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6.7k
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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
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
1
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1
reply
600
views
Analysis design for DESeq2
DifferentialExpression DESeq2
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
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
23 months ago giBio • 0
0
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1
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559
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How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
2
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1
reply
215
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 3 months ago by 41k • written 3 months ago by ▴ 20
1
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2
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855
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
12 months ago AZ ▴ 30
0
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2
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346
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
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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8
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1.5k
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Three conditions and two time points
DifferentialExpression DESeq2 time
2.6 years ago • updated 2.5 years ago AZ ▴ 30
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
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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1
reply
650
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Limma: how to make a table of logFC of certain genes (I need to define logFC of 62 genes specific for the cells of interest)
DifferentialExpression limma R TissueMicroarrayData
updated 16 months ago by 50k • written 16 months ago by • 0
1
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3
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923
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Not full rank DESeq2
DESeq2 DifferentialExpression
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
1
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2
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648
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 12 months ago by 50k • written 12 months ago by • 0
2
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4
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825
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Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 15 months ago by 41k • written 15 months ago by • 0
1
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2
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235
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
6 weeks ago • updated 5 weeks ago Chanderkant Chaudhary • 0
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Answer: Method to find pathways different between 2 groups by Gordon Smyth 50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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