Showing : DifferentialExpression • reset
0
votes
4
replies
1.0k
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
20 months ago sreeshmaraj72 • 0
2
votes
7
replies
4.2k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 17 months ago by • 0 • written 3.8 years ago by ▴ 20
1
vote
3
replies
763
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 months ago by • 0
3
votes
5
replies
6.4k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
3.4 years ago zhxiaokang ▴ 20
0
votes
3
replies
572
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 5 months ago by • 0
2
votes
6
replies
1.2k
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 15 months ago by 16k • written 15 months ago by • 0
0
votes
7
replies
1.5k
views
Which Limma guide is recommended ?
limma R DifferentialExpression
2.8 years ago • updated 2.7 years ago JAcky • 0
3
votes
3
replies
1.3k
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
2.9 years ago nhaus ▴ 70
3
votes
5
replies
1.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
0
votes
2
replies
598
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 10 months ago by 52k • written 10 months ago by • 0
3
votes
8
replies
4.5k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.7 years ago by ▴ 10
4
votes
10
replies
1.7k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
4.2 years ago Hajar • 0
1
vote
2
replies
1.0k
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 13 months ago by 52k • written 14 months ago by • 0
3
votes
5
replies
1.9k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 7 months ago by • 0 • written 10 months ago by ▴ 50
3
votes
6
replies
1.8k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 2.2 years ago by • 0
2
votes
8
replies
2.6k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.7 years ago Jane ▴ 10
2
votes
8
replies
2.6k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 19 months ago by ▴ 10
1
vote
3
replies
953
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 13 months ago by • 0
0
votes
3
replies
594
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 5 months ago by 52k • written 5 months ago by • 0
12
votes
13
replies
10k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 11 months ago by ★ 4.6k • written 2.9 years ago by ▴ 70
6
votes
3
replies
1.8k
views
differential gene expression
limma differentialexpression
updated 10.3 years ago by ▴ 760 • written 10.3 years ago by ▴ 20
6
votes
11
replies
1.9k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
23 months ago mohammedtoufiq91 ▴ 10
5
votes
9
replies
2.0k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 3.5 years ago by 67k • written 3.5 years ago by ▴ 840
1
vote
2
replies
1.3k
views
Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpression DESeq2 Normalization
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
0
votes
2
replies
1.8k
views
Comparison when Control is in differen batch
DESeq2 DifferentialExpression
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by ▴ 30
0
votes
3
replies
3.1k
views
Comparisons both between and within subjects using DESeq2
deseq2 edger differentialexpression
10.3 years ago asaferali • 0
0
votes
1
reply
1.8k
views
TCC::ERROR: Need the design matrix for GLM
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 10.8 years ago by ▴ 10 • written 10.8 years ago by 52k
5
votes
2
replies
3.0k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 2.4 years ago by 52k • written 3.4 years ago by ▴ 10
0
votes
3
replies
1.1k
views
Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
6
votes
5
replies
1.9k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 12 weeks ago by 52k • written 10 months ago by ▴ 50
0
votes
1
reply
789
views
Wald or LR Test
DESeq2 DifferentialExpression
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
2
votes
3
replies
1.7k
views
DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
votes
7
replies
3.3k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 4.2 years ago by 52k • written 4.2 years ago by ▴ 20
3
votes
7
replies
1.7k
views
Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 3.9 years ago by 52k • written 3.9 years ago by ▴ 30
4
votes
2
replies
7.1k
views
DESeq2: removing levels from a factor or not having them in the analysis at all
deseq2 differentialexpression
updated 10.3 years ago by 43k • written 10.3 years ago by ▴ 110
2
votes
4
replies
1.1k
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
votes
1
reply
410
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
0
votes
1
reply
839
views
Need of some clarifications
TimeCourse DifferentialExpression DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 30
5
votes
6
replies
2.2k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.9 years ago by ★ 28k • written 4.0 years ago by • 0
0
votes
1
reply
736
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 2.0 years ago by ★ 4.6k • written 2.0 years ago by • 0
1
vote
1
reply
728
views
Analysis design for DESeq2
DifferentialExpression DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
votes
3
replies
1.8k
views
Offsets and normalization in EdgeR
edgeR DifferentialExpression
updated 4.2 years ago by 52k • written 4.2 years ago by • 0
1
vote
2
replies
1.2k
views
Removing Unwanted Variations
DESeq2 NanoStringNCTools RUVnormalize RUVSeq DifferentialExpression
21 months ago AZ ▴ 30
3
votes
6
replies
1.9k
views
do I have to do this step in creating DGEList ?
DifferentialExpression
updated 23 months ago by 52k • written 23 months ago by • 0
2
votes
5
replies
685
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 6 months ago by 67k • written 6 months ago by • 0
0
votes
8
replies
1.9k
views
Three conditions and two time points
DifferentialExpression DESeq2 time
3.3 years ago • updated 3.2 years ago AZ ▴ 30
1
vote
2
replies
2.4k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.8 years ago Ismail • 0
1
vote
2
replies
877
views
DESeq2 with very large feature set
DESeq2 DifferentialExpression
4.2 years ago ramiro.barrantes ▴ 10
0
votes
1
reply
873
views
Limma: how to make a table of logFC of certain genes (I need to define logFC of 62 genes specific for the cells of interest)
DifferentialExpression limma R TissueMicroarrayData
updated 2.0 years ago by 52k • written 2.0 years ago by • 0
0
votes
2
replies
797
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
13 months ago Luca • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: WGCNA sample-data preprocessing order by ATpoint ★ 4.6k
Hi, WGCNA is not a Bioconductor package, please read the documentation to get guidance. See https://support.bioconductor.org/p/9155561/. …
Answer: WGCNA: Can we use high power (26) for signed network? by ATpoint ★ 4.6k
Hi, WGCNA is not a Bioconductor package, please read the documentation to get guidance. See https://support.bioconductor.org/p/9155561/. C…
Answer: Ph.D. scholar by ATpoint ★ 4.6k
Hi, WGCNA is not a Bioconductor package, please read the documentation to get guidance. See https://support.bioconductor.org/p/9155561/. C…
Comment: Recount3 data correspond to TCGA data by Fep29 • 0
Hi, This the solution to mapping TCGA ids in Recount3 to the ids used in the TCGA barcodes: library(recount3) human_projects <- …
Answer: Unable to find sample sheet file for ChAMP methylation data analysis by James W. MacDonald 67k
There is an example file in the extdata directory of the `minfiData` package that you could emulate.
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Awards • All
Popular Question to shepherl 4.1k
Popular Question to Martin Morgan 25k
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to Joseph Fass ▴ 70
Popular Question to Peter Hickey ▴ 750
Locations • All
United States, 21 minutes ago
Germany, 31 minutes ago
WEHI, Melbourne, Australia, 37 minutes ago
The Netherlands, 1 hour ago
Japan, 2 hours ago
Traffic: 742 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