Showing : differential gene expression • reset
5
votes
4
replies
3.6k
views
Why DESeq2 and edgeR give different results?
deseq2 rnaseq differential gene expression edger
updated 4.8 years ago by 53k • written 7.8 years ago by ▴ 120
3
votes
4
replies
2.3k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 7.8 years ago by 53k • written 7.8 years ago by • 0
5
votes
12
replies
11k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 7.8 years ago by 53k • written 7.8 years ago by ▴ 120
3
votes
3
replies
11k
views
TPM data Differential expression analysis
edger limma differential gene expression
updated 3.8 years ago by 53k • written 7.8 years ago by • 0
1
vote
3
replies
987
views
Differentially expressed genes detection between three classes with a batch effect in DESeq2
deseq2 batch effect differential gene expression
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
votes
1
reply
1.6k
views
Global Trend Analysis using results from EdgeR
EdgeR clustering differential gene expression consensusclusterplus kmeans
updated 7.8 years ago by ★ 29k • written 7.8 years ago by • 0
2
votes
4
replies
2.8k
views
Interpretation of cngeneson when doing differential expression analysis in MAST
mast differential gene expression
updated 7.9 years ago by ▴ 280 • written 7.9 years ago by ▴ 40
4
votes
4
replies
2.4k
views
Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
edger differential gene expression upregulated genes downregulated genes
updated 7.9 years ago by • 0 • written 7.9 years ago by ▴ 60
1
vote
5
replies
1.9k
views
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
7.9 years ago David R ▴ 90
1
vote
1
reply
1.4k
views
DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
votes
2
replies
4.0k
views
Going crazy with normalizing TCGA raw rsem gene count
cancer tcga normalization rnaseq differential gene expression
updated 7.9 years ago by • 0 • written 10.8 years ago by • 0
2
votes
0
replies
1.7k
views
Job: PhD Studentship - Investigating Regulation of Transcription and Translation in Prostate Cancer
mirna riboseq smallrna differential gene expression Job
8.0 years ago Andy Lynch ▴ 120
1
vote
4
replies
2.0k
views
Upregulation and Downregulation of Gene Ontology terms
microarray david differential gene expression GO
8.0 years ago seendey16 • 0
0
votes
1
reply
1.7k
views
Differential Coexpression Analysis
differential analysis differential gene expression coexpression correlation
updated 8.0 years ago by ★ 3.0k • written 8.0 years ago by ▴ 20
3
votes
3
replies
1.4k
views
edgeR multifactorial analysis implementation with RNA-Seq data
edger multifactorial design multiple comparisons differential gene expression
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 840
0
votes
0
replies
703
views
plotMA is not centered around zero for logFC
microarray differential gene expression
8.0 years ago twentestat • 0
1
vote
3
replies
1.8k
views
Clustering of samples based on specific gene sets
microarray differential gene expression gene set analysis clustering
8.0 years ago cherlyn.t • 0
0
votes
8
replies
7.0k
views
Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
8.0 years ago Marina ▴ 40
0
votes
1
reply
1.3k
views
Requesting help with RNA-Seq differential gene analysis
differential gene expression gene expression clustering gene regulatory network normalization
8.0 years ago sagnik • 0
0
votes
2
replies
4.6k
views
DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2 goseq rnaseq go enrichment differential gene expression
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
5
votes
5
replies
3.3k
views
Performing differential gene analysis on RT PCR experimental data
differential gene expression
updated 8.1 years ago by 53k • written 8.1 years ago by ▴ 10
1
vote
4
replies
1.1k
views
Pairwise Comparison between A Large Number of Groups
deseq2 differential gene expression
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
0
votes
1
reply
3.8k
views
DESeq2 design model/contrasts question 3 level condition
deseq2 model design differential gene expression experimental design
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
1
vote
2
replies
1.7k
views
Differential expression of RNA seq data at gene level (for Beginner)
deseq2 differential gene expression bioconductor
updated 8.2 years ago by ▴ 130 • written 8.2 years ago by • 0
2
votes
3
replies
2.2k
views
Can DESeq2/edgeR perform differential analysis for rRNA?
deseq2 edger rRNA differential gene expression
8.2 years ago r.aprianto ▴ 30
1
vote
2
replies
3.0k
views
RNA-seq read alignment best practices for low-input samples
limma differential gene expression rnaseq analysis alignment RSEM
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
0
votes
1
reply
1.2k
views
What package should I use to retrieve chromosome location for Affymetrix id of gene symbol id while doing gene expression microarray analysis ?
affymetrix microarrays differential gene expression
updated 8.2 years ago by 68k • written 8.2 years ago by ▴ 20
3
votes
1
reply
1.5k
views
Applying replaceOutliers rather than throwing out genes when model includes continuous variable
deseq2 rnaseq differential gene expression differential expression
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
2
votes
9
replies
2.6k
views
Loads, really loads of DEGs after edgeR differential analysis
rnaseq edger normalization differential gene expression
8.2 years ago David R ▴ 90
1
vote
5
replies
3.2k
views
Constant High Padj Values
deseq2 differential gene expression multiple factor design padj
updated 8.2 years ago by 43k • written 8.2 years ago by • 0
2
votes
9
replies
2.2k
views
SNP-level Allele-specific expression detection using DESeq2 in an unpaired experimental design
deseq2 rnaseq differential gene expression
8.3 years ago engelbrecht.stephan ▴ 10
0
votes
2
replies
2.7k
views
Differential expression between multiple groups
multiple groups differential gene expression microarray
8.3 years ago A ▴ 60
1
vote
7
replies
5.8k
views
deseq2 analysis with multiple factors and interaction terms
deseq2 multiple factor design differential analysis differential gene expression
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 10
0
votes
4
replies
1.9k
views
limma. After running a differential expression analysis... Can you get the individual gene expression levels between individual contrasts for each of…
limma gene expression differential gene expression
8.3 years ago arfranco ▴ 130
2
votes
4
replies
1.5k
views
Multiple differential expression analyses with DESeq2
deseq2 differential gene expression
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
1
vote
7
replies
2.1k
views
Strange distribution of logFC
edger deseq2 rnaseq differential gene expression
updated 8.3 years ago by ★ 29k • written 8.3 years ago by ▴ 20
0
votes
1
reply
2.3k
views
Ballgown with replicates and the adjustvars option
ballgown rnaseq differential gene expression
updated 8.3 years ago by ▴ 210 • written 8.5 years ago by • 0
4
votes
6
replies
29k
views
Design model for DESeq2 analysis
deseq2 differential gene expression
updated 8.3 years ago by ▴ 690 • written 8.3 years ago by ▴ 20
0
votes
3
replies
1.7k
views
Adding gene names which are differentially expressed in the plot
edgeR plot differential gene expression
8.3 years ago fawazfebin ▴ 60
1
vote
3
replies
2.5k
views
Differential Expression analysis between distinct scRNA-seq datasets
scrna scrnaseq differential gene expression
updated 8.3 years ago by ▴ 980 • written 8.3 years ago by • 0
0
votes
3
replies
1.9k
views
replicates and groups of samples: what's the right DESeq2 model?
deseq2 rnaseq differential gene expression
updated 8.4 years ago by ▴ 690 • written 8.4 years ago by • 0
0
votes
0
replies
857
views
comparison of expression between orthologous species
rnaseq differential gene expression
8.4 years ago laksharikrish • 0
4
votes
5
replies
1.8k
views
Differential gene expression: common changes in response to treatment across cell types
deseq2 differential gene expression
updated 8.4 years ago by ▴ 690 • written 8.4 years ago by ▴ 10
3
votes
6
replies
3.1k
views
Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix toptable makecontrasts differential gene expression
8.4 years ago stinehedensted • 0
0
votes
3
replies
1.9k
views
Differential expression of individual genes using edgeR
edger differential gene expression
8.4 years ago fawazfebin ▴ 60
4
votes
2
replies
1.7k
views
Differential gene expression for multi-factorial experiment using edgeR
edger differential gene expression multiple factor design
updated 8.4 years ago by ★ 29k • written 8.4 years ago by • 0
0
votes
5
replies
4.2k
views
Choosing genes for clustering
limma clustering differential gene expression hierarchical clustering feature selection
8.5 years ago • updated 8.4 years ago lirongrossmann ▴ 80
6
votes
19
replies
5.4k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 8.4 years ago by ▴ 690 • written 8.4 years ago by ▴ 50
2
votes
3
replies
2.5k
views
Differential expression of nomalised and log2 transformed data in limma
limma lmfit model.matrix differential gene expression
8.4 years ago stinehedensted • 0
0
votes
1
reply
2.2k
views
DESeq2 biological replicates and RIN values
deseq2 differential gene expression covariates rnaseq
updated 8.4 years ago by 43k • written 8.4 years ago by • 0
272 results • Page 2 of 6
Recent ...
Replies
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Awards • All
Popular Question to Jaqueline • 0
Scholar to Gordon Smyth 53k
Popular Question to Dario Strbenac ★ 1.6k
Popular Question to chirag.parsania ▴ 10
Popular Question to Michael Love 43k
Locations • All
Chile, 14 minutes ago
Barcelona, Spain, 23 minutes ago
Iran, 39 minutes ago
United States, 52 minutes ago
United States, 1 hour ago
Traffic: 1225 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