Showing : differentialexpression • reset
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
5 days ago • updated 2 days ago ktz • 0
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3
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586
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
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1
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171
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
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1
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251
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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5
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388
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 11 weeks ago by • 0
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408
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
4 months ago • updated 3 months ago Tadeoye ▴ 20
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9
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1.2k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 4 months ago by 68k • written 4 months ago by • 0
3
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3
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668
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 4 months ago by 52k • written 4 months ago by • 0
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579
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
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5
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851
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
0
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1
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309
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
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6
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1.1k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 5 months ago by 43k • written 6 months ago by • 0
0
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3
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701
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 7 months ago by 52k • written 7 months ago by • 0
3
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3
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1.1k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 7 months ago by 68k • written 7 months ago by • 0
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3
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728
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 7 months ago by • 0
3
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5
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1.7k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 7 months ago by ★ 1.4k • written 8 months ago by • 0
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3
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724
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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 8 months ago by ★ 4.8k • written 8 months ago by • 0
2
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5
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812
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 8 months ago by 68k • written 8 months ago by • 0
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0
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580
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
9 months ago nhaus ▴ 70
3
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5
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2.5k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 months ago by • 0 • written 13 months ago by ▴ 60
2
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1
reply
603
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 9 months ago by 68k • written 9 months ago by ▴ 70
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4
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791
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
10 months ago vohara4 • 0
0
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1
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467
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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 10 months ago by 68k • written 10 months ago by • 0
0
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3
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541
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 10 months ago by 43k • written 10 months ago by • 0
1
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3
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813
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 10 months ago by 52k • written 11 months ago by • 0
0
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1
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480
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
2
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7
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1.5k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
11 months ago sajadahmad41454 • 0
0
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3
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1.1k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
0
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3
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678
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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 11 months ago by 68k • written 11 months ago by • 0
0
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2
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629
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 12 months ago by 43k • written 12 months ago by ▴ 70
5
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6
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1.1k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 12 months ago by ★ 4.8k • written 12 months ago by ▴ 70
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3
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658
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 12 months ago by 68k • written 12 months ago by • 0
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2
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658
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 12 months ago by 68k • written 12 months ago by • 0
1
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2
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637
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
12 months ago Chanderkant Chaudhary • 0
8
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5
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2.4k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 months ago by 52k • written 12 months ago by ▴ 60
0
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2
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666
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 12 months ago by 52k • written 13 months ago by • 0
0
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2
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906
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 13 months ago by 43k • written 13 months ago by • 0
1
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3
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840
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 14 months ago by • 0
0
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4
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802
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
13 months ago mperalc • 0
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0
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612
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
13 months ago Abril • 0
2
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1
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605
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 13 months ago by ★ 4.8k • written 13 months ago by • 0
3
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2
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704
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
14 months ago Shaimaa Gamal • 0
4
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3
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886
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 14 months ago by 52k • written 14 months ago by • 0
2
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3
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825
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 14 months ago by 68k • written 14 months ago by • 0
2
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1
reply
547
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 14 months ago by 43k • written 14 months ago by ▴ 20
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2
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635
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 14 months ago by 43k • written 14 months ago by • 0
5
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6
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1.2k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
14 months ago Shaimaa Gamal • 0
4
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6
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1.3k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 14 months ago by 52k • written 15 months ago by • 0
3
votes
1
reply
675
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 15 months ago by 52k • written 15 months ago by • 0
1
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3
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1.1k
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 15 months ago by • 0
50 results • Page 1 of 1
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Comment: BiocParallel_1.40.1.tar.gz not available by Johan • 0
Your approach works, but it implies manually rejecting the update of BiocParallel at each use of `BiocManager::install()`, which is pretty …
Comment: BiocParallel_1.40.1.tar.gz not available by shepherl 4.1k
Thank you for your question. We are aware of the issue and are in process of resolving.
Comment: BiocParallel_1.40.1.tar.gz not available by Mike Smith ★ 6.6k
I'm not sure why the source package isn't currently available, but when you get the to question `Old packages: 'BiocParallel' Update all/so…
Answer: DNAStringSet(x, start=, end=) loses quality information by stenlana035 • 0
Perhaps the hub genes are associated with other variables that have a negative correlation with the immune score rather than the immunologi…
Answer: Model performance for spline modelling of RNA-seq timecourses in edgeR by Gordon Smyth 52k
I don't understand your question, because there is no difference between limma or glmFit or glmQLFit in terms of spline modeling or the tes…
Votes
Modelling gene program dynamics across time with {lemur}
A: DESeq2 one group vs multiple groups comparison in presence of batch effect
Comment: BiocParallel_1.40.1.tar.gz not available
Comment: BiocParallel_1.40.1.tar.gz not available
Limma outputs different results for same sample?
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