Showing : DifferentialExpression • reset
1
vote
2
replies
1.7k
views
Identifying presence of certain genes
DifferentialExpression TCGAWorkflow
3.9 years ago Sam ▴ 10
0
votes
1
reply
973
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by ▴ 30
0
votes
2
replies
1.3k
views
How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR DifferentialExpression TMM RNASeq
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
0
votes
2
replies
2.7k
views
Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
4.0 years ago p.l.chen • 0
2
votes
2
replies
9.0k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by ▴ 10
0
votes
8
replies
2.1k
views
Three conditions and two time points
DifferentialExpression DESeq2 time
4.0 years ago AZ ▴ 30
0
votes
1
reply
1.3k
views
Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 4.1 years ago by 43k • written 4.1 years ago by • 0
3
votes
5
replies
7.6k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
4.1 years ago zhxiaokang ▴ 20
1
vote
1
reply
796
views
Limma Experimental Design and Contrast Help (Identifying Differentially expressed genes with opposing patterns).
limma DifferentialExpression
updated 4.1 years ago by 53k • written 4.1 years ago by • 0
5
votes
4
replies
11k
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 3.5 years ago by • 0 • written 4.1 years ago by ▴ 10
0
votes
5
replies
1.7k
views
DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 3.1 years ago by 43k • written 4.1 years ago by • 0
5
votes
2
replies
3.5k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 3.1 years ago by 53k • written 4.2 years ago by ▴ 10
2
votes
4
replies
1.9k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
4.2 years ago mbenegas ▴ 10
1
vote
3
replies
1.5k
views
Not full rank DESeq2
DESeq2 DifferentialExpression
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
1
vote
1
reply
950
views
Different DESeq2 results
DESeq2 DifferentialExpression
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
2
replies
1.7k
views
Deseq2 outlier detection (about Cook's distance)
DESeq2 RNASeq DifferentialExpression
4.2 years ago peter.zhouyu • 0
5
votes
9
replies
2.3k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 840
0
votes
3
replies
1.3k
views
edgeR
edgeR DifferentialExpression
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
0
votes
6
replies
1.3k
views
DESeq2 time course confusion
DESeq2 DifferentialExpression
4.3 years ago rajpal22288 ▴ 10
2
votes
2
replies
2.3k
views
DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
4.3 years ago SUMIT • 0
2
votes
8
replies
2.9k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
4.4 years ago Jane ▴ 10
1
vote
3
replies
1.4k
views
The eBayes function gives two p-values for each row
hgu133plus2.db limma DifferentialExpression affy
updated 4.4 years ago by 53k • written 4.4 years ago by • 0
2
votes
2
replies
2.3k
views
Why does limma want log2 intensities but DESeq2 use raw counts?
limma DifferentialExpression DESeq2
4.4 years ago tjbencomo • 0
0
votes
2
replies
2.4k
views
Comparison when Control is in differen batch
DESeq2 DifferentialExpression
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by ▴ 30
0
votes
1
reply
949
views
Wald or LR Test
DESeq2 DifferentialExpression
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
2
votes
3
replies
2.1k
views
DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
3
votes
7
replies
1.9k
views
Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 4.6 years ago by 53k • written 4.6 years ago by ▴ 30
1
vote
0
replies
960
views
Design Matrix for multiple variables in Edge R
designmatrix DifferentialExpression edgeR RNAseq
4.6 years ago nageshprabhu.k ▴ 10
5
votes
6
replies
2.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 4.7 years ago by ★ 29k • written 4.7 years ago by • 0
1
vote
1
reply
820
views
Analysis design for DESeq2
DifferentialExpression DESeq2
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
vote
3
replies
1.5k
views
Error in Differential Expression Analysis with Data Set from Matrix
DESeq2 DifferentialExpression Bioconductor
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
votes
2
replies
2.0k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
4.8 years ago harelarik ▴ 60
3
votes
6
replies
1.8k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 50
1
vote
2
replies
1.4k
views
Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
votes
0
replies
1.1k
views
tissue specific differential expression using edgeR -- accounting for other effects in the model
edgeR DifferentialExpression
4.9 years ago Christy • 0
0
votes
7
replies
4.5k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 4.9 years ago by 53k • written 4.9 years ago by ▴ 20
1
vote
2
replies
987
views
DESeq2 with very large feature set
DESeq2 DifferentialExpression
4.9 years ago ramiro.barrantes ▴ 10
0
votes
3
replies
2.1k
views
Offsets and normalization in EdgeR
edgeR DifferentialExpression
updated 4.9 years ago by 53k • written 4.9 years ago by • 0
0
votes
1
reply
634
views
Using DESEQ/EdgeR for estimating differential expression relative to a control.
edgeR DifferentialExpression
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
4
votes
10
replies
2.0k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
5.0 years ago Hajar • 0
3
votes
6
replies
2.9k
views
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
6.0 years ago • updated 3.7 years ago hermidalc ▴ 20
2
votes
2
replies
2.5k
views
Normal Patient Samples from GSE62944
GSE62944 annotationhub differentialexpression
updated 9.5 years ago by ▴ 390 • written 9.5 years ago by • 0
0
votes
3
replies
3.3k
views
Comparisons both between and within subjects using DESeq2
deseq2 edger differentialexpression
11.0 years ago asaferali • 0
4
votes
2
replies
7.4k
views
DESeq2: removing levels from a factor or not having them in the analysis at all
deseq2 differentialexpression
updated 11.0 years ago by 43k • written 11.0 years ago by ▴ 110
6
votes
3
replies
1.9k
views
differential gene expression
limma differentialexpression
updated 11.0 years ago by ▴ 760 • written 11.0 years ago by ▴ 20
0
votes
1
reply
2.0k
views
TCC::ERROR: Need the design matrix for GLM
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 11.5 years ago by ▴ 10 • written 11.5 years ago by 53k
0
votes
1
reply
2.2k
views
TCC::ERROR: Need the design matrix for GLM.
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 11.5 years ago by ▴ 10 • written 11.5 years ago by ▴ 100
0
votes
1
reply
1.5k
views
read.maimages problem under sun ?
Microarray OneChannel TwoChannel DifferentialExpression Preprocessing QualityControl affy
18.4 years ago Amin Moghaddasi ▴ 130
198 results • Page 4 of 4
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Awards • All
Popular Question to Travis • 0
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to Joseph • 0
Locations • All
United States, 13 minutes ago
Denmark, 3 hours ago
The city by the bay, 4 hours ago
Seattle, WA, United States, 4 hours ago
United States, 5 hours ago
Traffic: 554 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6