Showing : differentialexpression • reset
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 18 days ago by ★ 4.8k • written 19 days ago by • 0
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8
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2.5k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
25 days ago • updated 22 days ago ktz • 0
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3
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625
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
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1
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198
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 11 weeks ago by 43k • written 11 weeks ago by • 0
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1
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287
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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5
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430
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 3 months ago by • 0
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2
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443
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
4 months ago Tadeoye ▴ 20
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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 5 months ago by • 0
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3
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696
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
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601
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
5 months ago abadgerw • 0
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5
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892
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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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328
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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 6 months ago by 43k • written 6 months ago by • 0
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3
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733
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 8 months ago by 52k • written 8 months ago by • 0
3
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3
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1.2k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 8 months ago by 68k • written 8 months ago by • 0
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3
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778
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 8 months ago by • 0
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5
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
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3
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758
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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 9 months ago by ★ 4.8k • written 9 months ago by • 0
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5
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848
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 9 months ago by 68k • written 9 months ago by • 0
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0
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604
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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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2.7k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 months ago by • 0 • written 14 months ago by ▴ 60
2
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1
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631
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 10 months ago by 68k • written 10 months ago by ▴ 70
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4
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826
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
10 months ago vohara4 • 0
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1
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481
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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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568
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 11 months ago by 43k • written 11 months ago by • 0
1
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3
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843
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 11 months ago by 52k • written 11 months ago by • 0
0
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1
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500
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
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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
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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 12 months ago by ★ 4.8k • written 12 months ago by • 0
0
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3
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703
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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 12 months ago by 68k • written 12 months ago by • 0
0
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2
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662
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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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1.2k
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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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677
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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
0
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2
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721
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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
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2
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655
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
13 months ago Chanderkant Chaudhary • 0
8
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5
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2.5k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 6 months ago by 52k • written 13 months ago by ▴ 60
0
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2
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688
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 13 months ago by 52k • written 13 months ago by • 0
0
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2
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952
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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
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3
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856
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 15 months ago by • 0
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4
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819
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
14 months ago mperalc • 0
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0
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630
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
14 months ago Abril • 0
2
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1
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625
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 14 months ago by ★ 4.8k • written 14 months ago by • 0
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2
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728
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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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916
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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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845
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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
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563
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 15 months ago by 43k • written 15 months ago by ▴ 20
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2
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648
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 15 months ago by 43k • written 15 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
15 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
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1
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693
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 15 months ago by 52k • written 15 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Comment: Module membership vs gene significance result and Modules-trait relationships re by Vinaya • 0
Hi. I am having the same issue, and haven't found a solution still.
Votes
Answer: CluserProfiler message "No gene can be mapped"
A: Minfi issue: return code from pthread_create() is 22
Comment: Filtering after DESeq
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
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