Showing : DifferentialExpression • reset
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Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 9 days ago by 43k • written 9 days ago by • 0
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6
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1.1k
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 11 weeks ago by • 0
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2
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331
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
11 weeks ago jamie.gearing ▴ 60
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4
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318
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
11 weeks ago Denise • 0
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1
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655
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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
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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 10 months ago by ★ 5.0k • written 10 months ago by • 0
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3.1k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
10 months ago ktz • 0
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3
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1.2k
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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
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1
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488
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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 12 months ago by • 0
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753
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
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5
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819
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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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801
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
14 months ago Tadeoye ▴ 20
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2.0k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 14 months ago by 68k • written 14 months ago by • 0
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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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1.0k
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
15 months ago • updated 14 months ago abadgerw • 0
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1.3k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
15 months ago • updated 14 months ago abadgerw • 0
0
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1
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570
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
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6
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1.5k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 15 months ago by 43k • written 16 months ago by • 0
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3
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1.1k
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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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1.9k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 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 18 months ago by • 0
3
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5
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2.7k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
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3
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1.1k
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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
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0
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904
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
19 months ago nhaus ▴ 70
3
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5
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4.0k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 19 months ago by • 0 • written 23 months ago by ▴ 60
2
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1
reply
920
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by ▴ 70
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4
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1.4k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
20 months ago vohara4 • 0
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1
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710
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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 20 months ago by 68k • written 20 months ago by • 0
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3
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853
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by • 0
1
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3
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1.2k
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 21 months ago by 53k • written 21 months ago by • 0
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1
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667
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 21 months ago by ★ 5.0k • written 21 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
21 months ago sajadahmad41454 • 0
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3
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1.7k
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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
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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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937
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 22 months ago by 43k • written 22 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 22 months ago by ★ 5.0k • written 22 months ago by ▴ 70
1
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3
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983
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 22 months ago by 68k • written 22 months ago by • 0
0
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2
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1.2k
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 22 months ago by 68k • written 22 months ago by • 0
1
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2
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953
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
22 months ago Chanderkant Chaudhary • 0
8
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5
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3.8k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 15 months ago by 53k • written 22 months ago by ▴ 60
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2
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929
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 23 months ago by 53k • written 23 months ago by • 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 23 months ago by 43k • written 23 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 2.0 years 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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821
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
24 months ago Abril • 0
2
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1
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847
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
3
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2
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1.2k
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
24 months ago Shaimaa Gamal • 0
4
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3
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1.3k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 2.0 years ago by 53k • written 2.0 years 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 2.0 years ago by 68k • written 2.0 years ago by • 0
202 results • Page 1 of 5
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Comment: Chip Seq Analysis of RNA Polymerase 2 by Tikaaaq2c • 0
Without proper scaling or an enrichment check , Pol 2 peaks can appear flat against the background. If the data remains noisy, you might w…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by Tikaaaq2c • 0
Organizing complex transcripts requires the same discipline as managing a digital library on a learning platform. Many researchers use a [S…
Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Votes
Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
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