Showing : Differential Expression • reset
2
votes
9
replies
2.4k
views
Limma: Defining the design matrix of a linear mixed model
rnaseq limma differential expression
7.3 years ago j.baldauf • 0
3
votes
4
replies
2.5k
views
How to find significantly stably expressed miRNA with DESeq2 DE results
deseq2 microrna differential expression stable expression
8.6 years ago mariakarand ▴ 20
22
votes
17
replies
7.3k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 3.0 years ago by 42k • written 5.9 years ago by ▴ 30
6
votes
4
replies
2.6k
views
discrepance in DESeq2 results with different design structures
deseq2 differential expression independent filtering pre-filtering design matrix
9.1 years ago • updated 9.0 years ago Assa Yeroslaviz ★ 1.5k
1
vote
5
replies
7.4k
views
DESeq2 and edgeR getting very different results
edger deseq2 differential expression
updated 6.4 years ago by ▴ 20 • written 6.4 years ago by • 0
8
votes
11
replies
2.4k
views
dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and…
dream variancePartition limma differential expression repeated measures
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 20
4
votes
4
replies
3.5k
views
DESeq2: Abnormally skewed distribution of p-values
deseq2 p-value distribution differential expression
8.8 years ago GFM ▴ 20
3
votes
5
replies
6.6k
views
Ballgown up and down regulated genes
ballgown differential expression
updated 7.1 years ago by • 0 • written 8.3 years ago by ▴ 10
5
votes
4
replies
1.2k
views
Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 6.1 years ago by 50k • written 6.1 years ago by • 0
5
votes
3
replies
4.0k
views
edgeR - how to convert DGELRT and other classes to .csv files
edgeR differential expression file conversion
updated 24 months ago by • 0 • written 8.2 years ago by ▴ 10
2
votes
5
replies
1.2k
views
Comparing across sets of regulated genes -- Strategies?
limma differential expression
updated 7.3 years ago by ▴ 730 • written 7.3 years ago by ▴ 30
3
votes
4
replies
2.9k
views
Protein differential Expression analysis
differential expression proteomics
updated 8 months ago by ★ 4.1k • written 6.4 years ago by • 0
4
votes
4
replies
1.4k
views
Differential expression on codelink data
r codelink differential expression
updated 9.0 years ago by ▴ 760 • written 9.0 years ago by ▴ 260
6
votes
5
replies
2.3k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
4.0 years ago hollandademello ▴ 20
2
votes
2
replies
694
views
edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 4.1 years ago by 50k • written 4.1 years ago by ▴ 20
3
votes
6
replies
1.3k
views
Question about edgeR usage with one case and multiple controls
edgeR differential expression without replicate
7.9 years ago gavin.oliver • 0
2
votes
7
replies
2.1k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
1
vote
3
replies
1.4k
views
Differential expressiong with two groups in BASiCS
BASiCS single-cell bayesian differential expression
updated 6.3 years ago by ▴ 10 • written 6.3 years ago by ▴ 10
6
votes
6
replies
1.8k
views
Can i set a path for readCodlinkSet()
r differential expression codelink
updated 8.9 years ago by ▴ 760 • written 8.9 years ago by ▴ 260
4
votes
6
replies
2.5k
views
Find if a covariate has effect on gene expression level using edgeR and DESeq2
edger deseq2 model matrix differential expression
7.7 years ago ta65 • 0
2
votes
2
replies
1.9k
views
Analysis of shRNA screen data
shrna edger deseq2 differential expression normalized counts
7.8 years ago Jane Merlevede ▴ 90
0
votes
3
replies
1.4k
views
Differential Expression of c.diff. microarray
arrayexpress differential expression
9.0 years ago SSK ▴ 10
4
votes
5
replies
3.3k
views
How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 10
1
vote
6
replies
3.4k
views
Two-way anova 2x2 design with limma
limma microarray differential expression
6.5 years ago damoros • 0
3
votes
4
replies
5.1k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
6.7 years ago David Requena ▴ 20
0
votes
17
replies
3.5k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 11 months ago by • 0 • written 6.6 years ago by • 0
5
votes
6
replies
1.3k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 4.7 years ago by ▴ 840 • written 4.7 years ago by ▴ 10
0
votes
1
reply
747
views
Find differentially expressed values
differential gene expression differential expression edgeR
updated 9.0 years ago by 50k • written 9.0 years ago by • 0
1
vote
1
reply
2.5k
views
EdgeR:Calculating differential expression within/between groups in nested designs
edger nested design matrix differential expression
updated 9.2 years ago by ★ 28k • written 9.2 years ago by • 0
3
votes
3
replies
1.5k
views
edgeR contrast formulation question
edger rnaseq differential expression
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by • 0
2
votes
1
reply
1.8k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 8.7 years ago by 42k • written 8.7 years ago by • 0
1
vote
4
replies
1.2k
views
Specifically expressed genes
DESeq2 specific expression rnaseq clustering differential expression
updated 9.0 years ago by 42k • written 9.0 years ago by • 0
1
vote
3
replies
1.4k
views
How different ploidy affect differential expression analysis with RNA-seq
ploidy normalization rna-seq differential expression assumption
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 90
5
votes
2
replies
7.3k
views
Ballgown vs (voom,edgeR,DESeq,limma)
limma rnaseq differential expression voom
updated 9.3 years ago by ▴ 210 • written 9.3 years ago by ▴ 50
1
vote
1
reply
1.3k
views
expression profiles between DESeq2 and Mfuzz
deseq2 mfuzz differential expression timecourse
updated 7.6 years ago by 42k • written 7.6 years ago by ★ 1.5k
3
votes
1
reply
1.7k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
2
votes
4
replies
8.6k
views
Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma differential expression design matrix error eset
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 20
1
vote
2
replies
1.9k
views
How to proceed with different degradation levels of RNA-seq samples?
degradation RNA-seq variability differential expression brain
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 90
3
votes
2
replies
6.2k
views
Trying to understand differential gene expression through Venn Diagrams from the 'limma' R package: why is there a number outside my diagram?
limma r venn diagram differential expression
updated 9.6 years ago by 65k • written 9.6 years ago by • 0
7
votes
10
replies
5.8k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 6.2 years ago by ▴ 30 • written 7.8 years ago by ▴ 50
4
votes
8
replies
1.9k
views
EdgeR: batches and samples over-specify system, how to contrast un-modeled variables?
edger glmlrt() differential expression design and contrast matrix
updated 8.9 years ago by 50k • written 8.9 years ago by • 0
1
vote
2
replies
1.0k
views
2-Factor Experiment in edgeR, Effect of no reps in one set and two reps in others
rnaseq edger differential expression dispersion
updated 7.6 years ago by ★ 7.9k • written 7.6 years ago by • 0
3
votes
5
replies
2.0k
views
DESeq2: Appropriate way to deal with knockouts in experiment design (RIPSeq)
deseq2 differential expression immunoprecipitation
updated 7.8 years ago by 42k • written 7.8 years ago by ▴ 40
2
votes
1
reply
898
views
edgeR - testing interaction in a scenario of 2 tissues and 2 ages
edgeR R differential gene expression differential expression
updated 7.9 years ago by ★ 28k • written 7.9 years ago by • 0
17
votes
4
replies
30k
views
RPKM, CPM and TMM
edger rnaseq differential expression
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 150
5
votes
3
replies
3.2k
views
Error when calculating DE using the classical approach in edgeR
edgeR differential expression rna-seq
updated 7.7 years ago by 50k • written 7.7 years ago by • 0
1
vote
2
replies
1.7k
views
Passing contrasts as a vector gives an error
r limma differential expression
updated 8.9 years ago by 50k • written 8.9 years ago by ▴ 260
3
votes
10
replies
3.9k
views
Differential expression analysis of already normalized sequence counts
differential expression normalization deseq2
updated 7.9 years ago by 42k • written 7.9 years ago by ▴ 20
4
votes
4
replies
2.5k
views
Two-class unpaired test using LIMMA
Limma SAM differential expression
updated 9.5 years ago by 65k • written 9.5 years ago by ▴ 310
2
votes
3
replies
3.3k
views
Analysis of RNA-seq time series with edgeR
edger rna-seq differential expression timecourse time course
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning by angelaesper43 • 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools by BioinfGuru ▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Ken C • 0
Popular Question to Johannes Rainer ★ 2.0k
Popular Question to Chris ▴ 10
Popular Question to Guido Hooiveld ★ 4.0k
Scholar to Michael Love 42k
Locations • All
Spain, 7 minutes ago
Spain, 10 minutes ago
Sweden, 20 minutes ago
Greece, 24 minutes ago
WEHI, Melbourne, Australia, 30 minutes ago
Traffic: 770 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