Showing : DifferentialExpression • reset
6
votes
2
replies
4.2k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 10
0
votes
1
reply
1.2k
views
limma on spectral data
limma Metabolomics DifferentialExpression POMA
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
2
votes
4
replies
1.4k
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
1
reply
879
views
How to find degraded genes but unaffected by condition in a time course RNAseq experiment ?
DESeq2 RNASeqData DifferentialExpression
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
0
votes
2
replies
1.7k
views
Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.9 years ago dqt • 0
0
votes
1
reply
1.1k
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 2.9 years ago by 53k • written 2.9 years ago by • 0
1
vote
3
replies
9.3k
views
Manually calculating log2 fold change values from DESeq2 normalized counts
DESeq2 DifferentialExpression
2.9 years ago Jayesh Kumar • 0
0
votes
3
replies
1.4k
views
Tissue Level Differential Expression Analysis
DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
2
replies
1.6k
views
Deseq2 and co-expression network normalization
DESeq2 Normalization DifferentialExpression r
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
1
vote
3
replies
1.8k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
3
votes
6
replies
2.1k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 3.0 years ago by • 0
3
votes
7
replies
2.9k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
votes
1
reply
2.4k
views
How to interpret MAST coefficients
DifferentialExpression MAST
updated 6 months ago by ▴ 10 • written 3.1 years ago by • 0
0
votes
1
reply
1.4k
views
How to subset a list of genes from a curated reference list of genes
R subset DifferentialExpression
updated 3.1 years ago by ▴ 780 • written 3.2 years ago by • 0
0
votes
7
replies
2.1k
views
Help with differential gene expression using Agilent Microarray data (from GEO database)
limma Paireddata DifferentialExpression
updated 3.1 years ago by 68k • written 3.2 years ago by • 0
0
votes
1
reply
2.0k
views
Does DeSeq2 make comparisons between all samples vs. all controls, or between matched samples and controls in different groups?
DESeq2 RNAseq bulk DifferentialExpression
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
1
vote
0
replies
1.4k
views
adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
3.2 years ago Kevin Gregory ▴ 10
0
votes
0
replies
895
views
weighting sample group
monocle SingleCell DifferentialExpression
3.2 years ago Sogand • 0
0
votes
1
reply
850
views
DESeq2 : LRT with factorial and continuous data
DESeq2 DifferentialExpression
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
votes
0
replies
1.2k
views
Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
3.3 years ago António Miguel de Jesus Domingues ▴ 510
0
votes
8
replies
2.1k
views
Swish log2FC NA output
swish fishpond DifferentialExpression
3.3 years ago jvandinter • 0
1
vote
3
replies
1.6k
views
LFC shrinkage setting negative LFC svalues to zero
DESeq2 DifferentialExpression apeglm
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
votes
2
replies
1.4k
views
Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression GeneExpression R enrichment DEGseq
updated 3.4 years ago by ★ 1.4k • written 3.4 years ago by • 0
1
vote
6
replies
1.9k
views
Error while running DESeq2
DifferentialExpression
3.4 years ago srikar • 0
0
votes
0
replies
1.2k
views
Differential expression with single cell data: any good two component (hurdle) models recently?
SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST
3.4 years ago Nik Tuzov ▴ 90
1
vote
8
replies
2.4k
views
edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
3.5 years ago giBio • 0
0
votes
1
reply
1.1k
views
Diffbind: different results on the same sample depending on contrast parameters
DifferentialExpression DiffBind
updated 3.5 years ago by ★ 5.2k • written 3.5 years ago by • 0
0
votes
4
replies
1.6k
views
Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
3.5 years ago S • 0
0
votes
1
reply
1.1k
views
Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
3
votes
8
replies
5.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.6 years ago by ▴ 10
1
vote
4
replies
1.5k
views
How to figure out the FC value from Limma
limma DEGseq DifferentialExpression
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
1
vote
1
reply
1.4k
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
limma lmfit R DifferentialExpression
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
1
vote
2
replies
1.7k
views
How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
2
votes
2
replies
1.7k
views
edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
3.6 years ago Sarah • 0
1
vote
2
replies
3.0k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
3.6 years ago Ismail • 0
0
votes
7
replies
2.0k
views
Which Limma guide is recommended ?
limma R DifferentialExpression
3.6 years ago JAcky • 0
3
votes
4
replies
2.0k
views
How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
3.7 years ago • updated 3.6 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.1k
views
Getting erros from dds
DifferentialExpression DESeq2
updated 3.7 years ago by ★ 1.4k • written 3.7 years ago by • 0
0
votes
7
replies
2.1k
views
DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 3.6 years ago by 43k • written 3.7 years ago by • 0
12
votes
13
replies
13k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 22 months ago by ★ 5.0k • written 3.7 years ago by ▴ 70
1
vote
1
reply
4.0k
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
2
votes
2
replies
1.8k
views
Complex contrasts in limma
RNASeq limma DifferentialExpression
3.7 years ago tcalvo ▴ 100
3
votes
3
replies
1.6k
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
3.8 years ago nhaus ▴ 70
1
vote
1
reply
2.1k
views
How to determine if limma can adjust for batch effect
BatchEffect limma sva DifferentialExpression
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by ▴ 70
4
votes
5
replies
2.5k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 3.6 years ago by • 0 • written 3.8 years ago by ▴ 70
0
votes
2
replies
2.6k
views
Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
0
votes
0
replies
706
views
Error in DEqMS proteomics analysis
DEqMS R DifferentialExpression
3.8 years ago Mrinal.singh06 • 0
4
votes
3
replies
1.8k
views
Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
votes
2
replies
1.4k
views
Removing paired samples for DESeq2 analysis
RNASeq DifferentialExpression DESeq2 tcga
3.9 years ago IamFrofro • 0
0
votes
5
replies
2.5k
views
Weird output of DESeq2 when using single sample from one group agains the other group (6 samples), really need some help
DifferentialExpression DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 10
201 results • Page 3 of 5
Recent ...
Replies
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
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
Locations • All
The city by the bay, 23 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Ireland, 2 hours ago
United States, 3 hours ago
Pakistan, 3 hours ago
Traffic: 513 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