Showing : DifferentialExpression • reset
0
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4
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170
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
2 days ago georgeyu703 • 0
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2
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312
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
6 weeks ago Tadeoye ▴ 20
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9
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921
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 7 weeks ago by 67k • written 7 weeks ago by • 0
3
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3
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575
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 9 weeks ago by 52k • written 9 weeks ago by • 0
1
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3
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476
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
10 weeks ago • updated 8 weeks ago abadgerw • 0
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5
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687
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
10 weeks ago • updated 7 weeks ago abadgerw • 0
0
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1
reply
220
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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6
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894
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 12 weeks ago by 43k • written 3 months ago by • 0
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3
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594
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 5 months ago by 52k • written 5 months ago by • 0
3
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3
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852
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
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3
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572
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 5 months ago by • 0
3
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5
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1.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
0
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3
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617
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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 6 months ago by ★ 4.6k • written 6 months ago by • 0
2
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5
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685
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 6 months ago by 67k • written 6 months ago by • 0
0
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0
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472
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
6 months ago nhaus ▴ 70
3
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5
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1.9k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 7 months ago by • 0 • written 10 months ago by ▴ 50
2
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1
reply
482
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by ▴ 70
0
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4
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662
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
7 months ago vohara4 • 0
0
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1
reply
393
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
0
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3
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458
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 8 months ago by 43k • written 8 months ago by • 0
1
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3
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700
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 8 months ago by 52k • written 8 months ago by • 0
0
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1
reply
410
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
2
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7
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1.2k
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
8 months ago sajadahmad41454 • 0
0
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3
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879
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
0
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3
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590
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 8 months ago by 67k • written 8 months ago by • 0
0
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2
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554
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 9 months ago by 43k • written 9 months ago by ▴ 70
5
votes
6
replies
953
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 9 months ago by ★ 4.6k • written 9 months ago by ▴ 70
1
vote
3
replies
591
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 9 months ago by 67k • written 9 months ago by • 0
0
votes
2
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521
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 9 months ago by 67k • written 9 months ago by • 0
1
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2
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545
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
10 months ago Chanderkant Chaudhary • 0
6
votes
5
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1.9k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 12 weeks ago by 52k • written 10 months ago by ▴ 50
0
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2
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598
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 10 months ago by 52k • written 10 months ago by • 0
0
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2
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763
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 10 months ago by 43k • written 10 months ago by • 0
1
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3
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763
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 months ago by • 0
0
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4
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712
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 months ago • updated 10 months ago mperalc • 0
0
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0
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544
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 months ago Abril • 0
2
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1
reply
547
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
3
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2
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624
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 months ago Shaimaa Gamal • 0
4
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3
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779
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 months ago by 52k • written 11 months ago by • 0
2
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3
replies
726
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 months ago by 67k • written 11 months ago by • 0
2
votes
1
reply
485
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 11 months ago by 43k • written 11 months ago by ▴ 20
0
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2
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578
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 11 months ago by 43k • written 11 months ago by • 0
5
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6
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1.1k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 months ago Shaimaa Gamal • 0
4
votes
6
replies
1.2k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 months ago by 52k • written 12 months ago by • 0
3
votes
1
reply
621
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 12 months ago by 52k • written 12 months ago by • 0
1
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3
replies
953
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 13 months ago by • 0
0
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5
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1.1k
views
Help with model for differential expression analysis
DifferentialExpression edgeR
13 months ago • updated 12 months ago Lucy ▴ 60
0
votes
3
replies
762
views
DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
1
vote
1
reply
683
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
2
votes
4
replies
914
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 12 months ago by 52k • written 13 months ago by • 0
50 results • Page 1 of 1
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