Showing : DifferentialExpression • reset
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Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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8
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DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
3.9 years ago dadca596 • 0
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997
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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 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 4.2 years ago by 53k • written 4.2 years ago by • 0
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2
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
4.2 years ago p.l.chen • 0
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2
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Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 4.2 years ago by ★ 5.0k • written 4.2 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
4.2 years ago • updated 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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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 4.3 years ago by 53k • written 4.3 years ago by • 0
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4
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11k
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DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 3.7 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 3.3 years ago by 53k • written 4.3 years ago by ▴ 10
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4
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2.0k
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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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983
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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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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 4.4 years ago by 68k • written 4.4 years ago by ▴ 840
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3
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1.4k
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edgeR
edgeR DifferentialExpression
updated 4.4 years ago by 53k • written 4.4 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
4.5 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 4.6 years ago by 53k • written 4.6 years ago by • 0
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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
4.6 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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995
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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 4.8 years ago by 43k • written 4.8 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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996
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Design Matrix for multiple variables in Edge R
designmatrix DifferentialExpression edgeR RNAseq
4.8 years ago nageshprabhu.k ▴ 10
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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
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1
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857
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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 5.0 years ago by • 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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1.2k
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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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4.7k
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topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 5.1 years ago by 53k • written 5.1 years ago by ▴ 20
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DESeq2 with very large feature set
DESeq2 DifferentialExpression
5.1 years ago ramiro.barrantes ▴ 10
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3
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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
0
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660
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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
6.2 years ago • updated 3.9 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
4
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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 11.2 years ago by 43k • written 11.2 years ago by ▴ 110
6
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3
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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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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
201 results • Page 4 of 5
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Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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