Showing : DifferentialExpression • reset
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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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4
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730
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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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Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
2.2 years ago • updated 2.1 years ago nhaus ▴ 30
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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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3.3k
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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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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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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
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2
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254
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
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9
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1.5k
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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 2.7 years ago by ▴ 830
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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
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7
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1.2k
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Which Limma guide is recommended ?
limma R DifferentialExpression
2.0 years ago • updated 24 months ago JAcky • 0
4
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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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3
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358
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
2
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6
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753
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 6 months ago by 16k • written 6 months ago by • 0
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3
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567
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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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4.7k
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How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
2.6 years ago zhxiaokang ▴ 20
9
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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
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
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1.1k
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Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 3.4 years ago by 41k • written 3.4 years ago by • 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 10.0 years ago by ▴ 10 • written 10.0 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 3.4 years ago by 50k • written 3.4 years ago by ▴ 20
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
0
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1
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669
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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
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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
0
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3
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842
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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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681
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 27 days ago by 50k • written 4 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 2.2 years ago by 65k • written 2.2 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 19 months ago by 41k • written 2.7 years ago by • 0
1
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2
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653
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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
596
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
22 months ago giBio • 0
0
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1
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553
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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 ★ 4.0k • written 15 months ago by • 0
2
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1
reply
206
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 11 weeks ago by 41k • written 11 weeks ago by ▴ 20
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2
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829
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Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
12 months ago AZ ▴ 30
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2
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320
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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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1.4k
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Three conditions and two time points
DifferentialExpression DESeq2 time
2.6 years ago • updated 2.5 years ago AZ ▴ 30
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
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639
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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 15 months ago by 50k • written 15 months ago by • 0
1
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3
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907
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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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628
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 11 months ago by 50k • written 11 months ago by • 0
2
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4
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804
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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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211
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
4 weeks ago • updated 28 days ago Chanderkant Chaudhary • 0
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by marka • 0
As a single dad in Australia, finding time to unwind is rare, but [Lincoln Casino][1] has become my go-to escape after putting the kids to …
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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