Showing : differentialexpression • reset
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Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
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8
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2.9k
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DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
3.9 years ago dadca596 • 0
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992
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NanoStringDiff
DifferentialExpression NanoStringDiff
4.0 years ago sanrie10 • 0
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1.7k
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Identifying presence of certain genes
DifferentialExpression TCGAWorkflow
4.1 years ago • updated 4.0 years ago Sam ▴ 10
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1.0k
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Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by ▴ 30
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1.4k
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How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR DifferentialExpression TMM RNASeq
updated 4.1 years ago by 53k • written 4.1 years ago by • 0
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
4.1 years ago p.l.chen • 0
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2
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9.1k
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Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 4.1 years ago by ★ 5.0k • written 4.1 years ago by ▴ 10
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8
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2.2k
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Three conditions and two time points
DifferentialExpression DESeq2 time
4.1 years ago AZ ▴ 30
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1.4k
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Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
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5
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How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
4.2 years ago zhxiaokang ▴ 20
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Limma Experimental Design and Contrast Help (Identifying Differentially expressed genes with opposing patterns).
limma DifferentialExpression
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
5
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4
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11k
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DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 3.6 years ago by • 0 • written 4.3 years ago by ▴ 10
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5
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1.7k
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DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 3.2 years ago by 43k • written 4.3 years ago by • 0
5
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3.5k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 3.2 years ago by 53k • written 4.3 years ago by ▴ 10
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4
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1.9k
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edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
4.3 years ago mbenegas ▴ 10
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3
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1.5k
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Not full rank DESeq2
DESeq2 DifferentialExpression
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
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1
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976
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Different DESeq2 results
DESeq2 DifferentialExpression
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
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2
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1.8k
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Deseq2 outlier detection (about Cook's distance)
DESeq2 RNASeq DifferentialExpression
4.3 years ago peter.zhouyu • 0
5
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9
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2.4k
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Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 4.3 years ago by 68k • written 4.3 years ago by ▴ 840
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3
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1.4k
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edgeR
edgeR DifferentialExpression
updated 4.3 years ago by 53k • written 4.3 years ago by • 0
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6
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1.3k
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DESeq2 time course confusion
DESeq2 DifferentialExpression
4.4 years ago rajpal22288 ▴ 10
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2.4k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
4.4 years ago SUMIT • 0
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3.0k
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
4.5 years ago Jane ▴ 10
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1.5k
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The eBayes function gives two p-values for each row
hgu133plus2.db limma DifferentialExpression affy
updated 4.5 years ago by 53k • written 4.5 years ago by • 0
2
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2
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2.3k
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Why does limma want log2 intensities but DESeq2 use raw counts?
limma DifferentialExpression DESeq2
4.5 years ago tjbencomo • 0
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2
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2.4k
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Comparison when Control is in differen batch
DESeq2 DifferentialExpression
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 30
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1
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990
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Wald or LR Test
DESeq2 DifferentialExpression
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
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3
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2.1k
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DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
3
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7
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2.0k
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Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 4.8 years ago by 53k • written 4.8 years ago by ▴ 30
1
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0
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988
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Design Matrix for multiple variables in Edge R
designmatrix DifferentialExpression edgeR RNAseq
4.8 years ago nageshprabhu.k ▴ 10
5
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6
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2.7k
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DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 4.8 years ago by ★ 29k • written 4.8 years ago by • 0
1
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1
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852
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Analysis design for DESeq2
DifferentialExpression DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
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3
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1.6k
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Error in Differential Expression Analysis with Data Set from Matrix
DESeq2 DifferentialExpression Bioconductor
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
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2
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2.0k
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How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
5.0 years ago harelarik ▴ 60
3
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6
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1.9k
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Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 50
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1.5k
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Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
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0
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1.1k
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tissue specific differential expression using edgeR -- accounting for other effects in the model
edgeR DifferentialExpression
5.0 years ago Christy • 0
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7
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4.6k
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topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 20
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1.0k
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DESeq2 with very large feature set
DESeq2 DifferentialExpression
5.0 years ago ramiro.barrantes ▴ 10
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2.1k
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Offsets and normalization in EdgeR
edgeR DifferentialExpression
updated 5.1 years ago by 53k • written 5.1 years ago by • 0
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1
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657
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Using DESEQ/EdgeR for estimating differential expression relative to a control.
edgeR DifferentialExpression
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
4
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10
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2.1k
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Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
5.1 years ago Hajar • 0
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6
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3.0k
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Repeated measures per individual and unbalanced number of measures per individual: DE between groups still an ordinary two-group comparison?
differentialexpression deseq2 limma edger repeatedmeasures
6.1 years ago • updated 3.8 years ago hermidalc ▴ 20
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Normal Patient Samples from GSE62944
GSE62944 annotationhub differentialexpression
updated 9.7 years ago by ▴ 390 • written 9.7 years ago by • 0
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3.3k
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Comparisons both between and within subjects using DESeq2
deseq2 edger differentialexpression
11.1 years ago asaferali • 0
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2
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7.4k
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DESeq2: removing levels from a factor or not having them in the analysis at all
deseq2 differentialexpression
updated 11.1 years ago by 43k • written 11.1 years ago by ▴ 110
6
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2.0k
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differential gene expression
limma differentialexpression
updated 11.2 years ago by ▴ 760 • written 11.2 years ago by ▴ 20
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1
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2.0k
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TCC::ERROR: Need the design matrix for GLM
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 11.6 years ago by ▴ 10 • written 11.6 years ago by 53k
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TCC::ERROR: Need the design matrix for GLM.
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 11.6 years ago by ▴ 10 • written 11.6 years ago by ▴ 100
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