Showing : differentialexpression • reset
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 9 weeks ago by • 0
2
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2
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315
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
9 weeks ago jamie.gearing ▴ 60
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4
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285
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
9 weeks ago Denise • 0
0
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1
reply
634
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 8 months ago by 43k • written 8 months ago by • 0
1
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1
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1.4k
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
1
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
9 months ago ktz • 0
0
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3
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1.1k
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
0
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1
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475
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 11 months ago by 43k • written 11 months ago by • 0
0
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1
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728
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
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5
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802
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 12 months ago by • 0
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2
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783
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
13 months ago Tadeoye ▴ 20
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1.9k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 13 months ago by 68k • written 13 months ago by • 0
3
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3
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1.0k
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
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971
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
14 months ago abadgerw • 0
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5
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1.3k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
14 months ago • updated 13 months ago abadgerw • 0
0
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1
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564
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
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6
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 15 months ago by 43k • written 15 months ago by • 0
0
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3
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1.0k
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 17 months ago by 53k • written 17 months ago by • 0
3
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3
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1.8k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
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3
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1.2k
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 17 months ago by • 0
3
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5
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
0
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3
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1.0k
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
2
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5
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1.2k
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
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0
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866
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
18 months ago nhaus ▴ 70
3
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5
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3.8k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 19 months ago by • 0 • written 22 months ago by ▴ 60
2
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1
reply
891
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by ▴ 70
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4
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1.3k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
19 months ago vohara4 • 0
0
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1
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695
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
0
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3
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841
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by • 0
1
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3
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1.1k
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 20 months ago by 53k • written 20 months ago by • 0
0
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1
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661
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
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7
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2.1k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
20 months ago sajadahmad41454 • 0
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3
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1.6k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
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3
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1.0k
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 21 months ago by 68k • written 21 months ago by • 0
0
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2
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920
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by ▴ 70
5
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6
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1.6k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 21 months ago by ★ 5.0k • written 21 months ago by ▴ 70
1
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3
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971
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 21 months ago by 68k • written 21 months ago by • 0
0
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2
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1.1k
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 21 months ago by 68k • written 21 months ago by • 0
1
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2
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929
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
22 months ago Chanderkant Chaudhary • 0
8
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5
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3.6k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 14 months ago by 53k • written 22 months ago by ▴ 60
0
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2
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922
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 22 months ago by 53k • written 22 months ago by • 0
0
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2
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1.3k
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 22 months ago by 43k • written 22 months ago by • 0
1
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3
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1.1k
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 24 months ago by • 0
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4
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1.1k
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
23 months ago mperalc • 0
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0
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803
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
23 months ago Abril • 0
2
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1
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841
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
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2
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1.1k
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
23 months ago Shaimaa Gamal • 0
4
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3
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1.2k
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 23 months ago by 53k • written 23 months ago by • 0
2
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3
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1.2k
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 23 months ago by 68k • written 23 months ago by • 0
2
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1
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805
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 23 months ago by 43k • written 24 months ago by ▴ 20
201 results • Page 1 of 5
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Comment: Combining two proteomics datasets with limpa by Andrew Pattison • 0
Thanks heaps Gordon. I went with option 1 and no normalisation and all seems to have worked well. Cheers, Andrew
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
Flagging protein groups as likely contaminants in this way will be fine for a limpa analysis. The `Cont_` proteins can optionally stay in f…
Answer: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
Aaron Lun was a PhD student in my Lab back in 2015, when he posted the answers about allele-specific expression that you and Mike Love have…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
You just need the mouse identifier (controls baseline) and the group specific allelic effect.
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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