Showing : EdgeR • reset
0
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3
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1.2k
views
Is it allowed to fit two models to make between and within subjects comparisons separately?
rnaseq limma edger deseq2 random effects
6.7 years ago tcalvo ▴ 100
2
votes
2
replies
2.1k
views
Different DEG results using Ballgown and edgeR
edger ballgown rnaseq batch effect adjustvars
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
2
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2
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1.3k
views
edgeR DEG how many treatments should be fitted to GLM
edgeR GLM
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 10
2
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2
replies
2.4k
views
edgeR DEG sample size
minimum samples edgeR
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 10
1
vote
6
replies
2.2k
views
edgeR for time series
edgeR
updated 6.8 years ago by 53k • written 6.8 years ago by ▴ 40
6
votes
14
replies
3.6k
views
Paired analysis setup using edgeR - follow up question
edger
6.8 years ago candida.vaz ▴ 50
1
vote
3
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1.5k
views
Setting up the design for paired analysis
edger limma paired design
6.9 years ago • updated 6.8 years ago candida.vaz ▴ 50
1
vote
2
replies
1.4k
views
Aclaration of batch effect adjust in DE analysis
edger rnaseq batch effect
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
4
votes
4
replies
3.1k
views
Average read counts and batch-effect correction in edgeR
edgeR batch-effect RNA-seq read counts ngs
updated 6.8 years ago by ★ 29k • written 6.8 years ago by ▴ 20
12
votes
4
replies
5.2k
views
differential expression analysis of htseq data with edgeR/voom
voom htseq edgeR limma RNASeq123
updated 6.8 years ago by 53k • written 8.4 years ago by ▴ 30
2
votes
8
replies
5.3k
views
MDS Plot help in edgeR
edgeR plotmds differential gene expression MDS mdsplot
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
12
votes
12
replies
3.2k
views
FDR does not change between genes in edgeR
RNAseq edgeR
updated 6.8 years ago by 53k • written 6.8 years ago by ▴ 30
5
votes
14
replies
2.9k
views
Odd P-value distribution in edgeR on RRBS data
edgeR rrbs
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
3
votes
1
reply
2.0k
views
How to quantify or decide whether a covariate should be included in the linear model for differential expression analysis ?
limma edgeR deseq2
updated 6.8 years ago by 68k • written 6.8 years ago by ▴ 30
5
votes
1
reply
5.9k
views
RNAseq analysis: what comes first, filtering or normalization
edger R rnaseq
updated 6.8 years ago by ★ 29k • written 6.8 years ago by ▴ 30
3
votes
4
replies
2.5k
views
Implications of TMM Normalization and Possible Alternatives
edger TMM DEG normalization
updated 6.8 years ago by 53k • written 6.8 years ago by ▴ 30
2
votes
3
replies
1.1k
views
CalcNormFactors in Edge r
edger
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
0
votes
2
replies
1.0k
views
Remove "no_feature" and "alignment_not_unique" counts before using EdgeR or Deseq2
edger deseq2
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
0
votes
2
replies
1.7k
views
EstimateDisp and glm
edger
updated 6.8 years ago by ★ 29k • written 6.8 years ago by • 0
2
votes
1
reply
985
views
Help with multi-factored RNA-seq edgeR model
edger design model interaction model rnaseq
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
3
votes
5
replies
2.0k
views
Normalization for small non-coding RNA and multi-factor design
edger limma voom normalization limma
updated 6.8 years ago by 68k • written 6.8 years ago by ▴ 90
0
votes
7
replies
3.4k
views
Count filter for differential expression
edger limma counts
updated 6.9 years ago by 53k • written 6.9 years ago by • 0
2
votes
4
replies
1.9k
views
edgeR. Known cancer genes are not differentially expressed?
edger tcga
updated 6.9 years ago by ★ 29k • written 6.9 years ago by ▴ 30
2
votes
2
replies
1.5k
views
edgeR DE analysis: single group combined factors or GLM with interaction term
edger glm
updated 6.9 years ago by ★ 29k • written 6.9 years ago by ▴ 10
5
votes
2
replies
3.6k
views
non-integer counts for edgeR
edgeR
13.4 years ago • updated 6.9 years ago Gordon Smyth 53k
2
votes
4
replies
2.8k
views
Filtering, minimum sample number, and condition in edgeR
edger filtering
updated 6.9 years ago by ★ 7.9k • written 6.9 years ago by ▴ 30
5
votes
2
replies
2.1k
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport edgeR rna-seq
updated 6.9 years ago by 68k • written 6.9 years ago by • 0
6
votes
10
replies
4.6k
views
edgeR paired samples with blocking
limma edger blocking paired samples
updated 6.9 years ago by 53k • written 6.9 years ago by ▴ 10
2
votes
1
reply
1.2k
views
EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
edgeR design matrix contrast
updated 6.9 years ago by 53k • written 6.9 years ago by • 0
1
vote
5
replies
2.5k
views
edgeR: boxplot the expression of a gene in two conditions after glmFit
edgeR
updated 6.9 years ago by ★ 29k • written 6.9 years ago by ▴ 10
1
vote
9
replies
2.2k
views
shRNA-Seq analysis using edgeR
shrnaseq edger experimental design model.matrix
updated 6.9 years ago by ★ 29k • written 6.9 years ago by ★ 1.5k
3
votes
3
replies
3.1k
views
Change default prior.count in glmFit() to match cpm(), aveLogCPM(), etc?
edgeR prior.count
updated 6.9 years ago by 53k • written 6.9 years ago by ★ 2.0k
4
votes
2
replies
1.1k
views
EdgeR applied to peptide screen: help!
edger calcnormfactors peptide screen library size factor
updated 6.9 years ago by 53k • written 6.9 years ago by • 0
0
votes
1
reply
2.2k
views
edgeR 2-way ANOVA testing
edger ANOVA
updated 6.9 years ago by 53k • written 6.9 years ago by • 0
6
votes
4
replies
6.3k
views
Method to get normalized counts in edgeR without cpm
edger normalization
updated 6.9 years ago by 53k • written 6.9 years ago by ▴ 20
0
votes
1
reply
1.4k
views
RNAseq gene expression analysis in Personalized genomics
TCGA deseq2 edger limma
updated 6.9 years ago by 43k • written 7.0 years ago by • 0
2
votes
2
replies
1.7k
views
EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger design matrix glmlrt() glmQFTest() paired design
7.0 years ago oakhamwolf • 0
3
votes
3
replies
1.6k
views
Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat
updated 7.0 years ago by 53k • written 7.0 years ago by ▴ 840
2
votes
2
replies
1.6k
views
p -values smaller than machine epsilon in edgeR
edger p values
updated 7.0 years ago by 53k • written 7.0 years ago by • 0
3
votes
2
replies
1.5k
views
EdgeR - blocking for multiple factors at once - Errors
EdgeR multiple factor design blocked design
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 10
1
vote
11
replies
4.1k
views
edgeR package fails to load after install
edger install error
updated 7.0 years ago by ★ 29k • written 7.0 years ago by • 0
2
votes
5
replies
1.3k
views
Predict circadian expression with edgeR
edgeR circadian rhythms limorhyde
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 40
2
votes
3
replies
1.8k
views
Multi-factor with interaction model in EdgeR and DESeq2
edger deseq2 rnaseq differential gene expression
updated 7.0 years ago by 43k • written 7.0 years ago by • 0
9
votes
5
replies
6.5k
views
Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 7.0 years ago by ★ 13k • written 7.0 years ago by • 0
1
vote
4
replies
2.6k
views
model matrix for edgeR paired-design with batch effect
edgeR paired samples batch effect
updated 7.0 years ago by ★ 29k • written 7.0 years ago by • 0
0
votes
2
replies
940
views
Help with edgeR code - RNA-Seq Differental Gene Expression
edger rnaseq
updated 7.0 years ago by 53k • written 7.0 years ago by • 0
1
vote
2
replies
912
views
Dispersion & FDR in edgeR
edger R
updated 7.0 years ago by ★ 29k • written 7.0 years ago by • 0
2
votes
14
replies
3.0k
views
Differentiating between batch and treatment effects in edgeR, DESeq2
rnaseq batch effect deseq2 edger
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 30
1
vote
2
replies
1.6k
views
cohen's d in edgeR
edger effect size cohen d
updated 7.0 years ago by ★ 29k • written 7.0 years ago by ▴ 370
0
votes
4
replies
2.8k
views
PCA plot of variance stabilized transformation of normalized counts in limma
limma-voom deseq2 EdgeR
updated 7.0 years ago by ★ 13k • written 7.0 years ago by ▴ 20
2,031 results • Page 14 of 41
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Replies
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
R-4.5.1 is compatible with both release and devel versions of Bioconductor. Which one are you using? I am still on release, and it's fine: …
Votes
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
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