Showing : EdgeR • reset
3
votes
3
replies
1.2k
views
edgeR: the F-statistics changed after removing lowly expressed gene
glmQLFTest edgeR
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
1
vote
1
reply
693
views
could edgeR be applied to gene counts by gene family to make group comparisons?
edgeR
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
2
votes
6
replies
2.0k
views
Variance explained (coefficient of determination) in edgeR
edgeR
3.4 years ago Gemma • 0
2
votes
2
replies
1.6k
views
edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
3.4 years ago Sarah • 0
0
votes
2
replies
1.1k
views
Variance explained (coefficient of determination) in glmFit / glmLRT
edgeR
3.4 years ago Gemma • 0
0
votes
1
reply
1.7k
views
How to directly decet the outlier samples (libraries) in EdgeR pipeline
edgeR
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 30
5
votes
14
replies
7.3k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 3.4 years ago by ★ 5.0k • written 7.3 years ago by ▴ 60
0
votes
0
replies
751
views
diffcyt - topTable function returns one total significance estimate instead of one per comparison
limma diffcyt edgeR
3.5 years ago stefanos.bamopoulos • 0
1
vote
1
reply
1.3k
views
Should I keep libsizes?
Normalization edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
2
votes
7
replies
2.0k
views
edgeR: topTags weird behavior - outputting NAs
edgeR
3.5 years ago • updated 3.4 years ago venura • 0
0
votes
2
replies
1.5k
views
edgeR: Analyzing multiple factors with batch effects
edgeR
3.5 years ago venura • 0
0
votes
11
replies
3.2k
views
EdgeR function nearestTSS() fails with org.Ss.eg.db
Sus_scrofa edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
votes
4
replies
1.5k
views
Extremely different results for both EdgeR and DESeq2 analysis
edgeR DESeq2
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
2
votes
5
replies
1.5k
views
edgeR: Combining time series analysis with mock and treated samples
edgeR
3.5 years ago venura • 0
0
votes
2
replies
987
views
edgeR
rnaseq edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
votes
11
replies
2.4k
views
Differential methilation analysis - Design matrix not of full rank
DifferentialMethylation RRBSdata edgeR
updated 3.4 years ago by 53k • written 3.5 years ago by • 0
5
votes
6
replies
4.2k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools edgeR pcaExplorer RNASeq RNAseq123
3.5 years ago Alan • 0
0
votes
1
reply
1.8k
views
Differential methilation analysis batch effect removal
BatchEffect combat sva edgeR RRBSdata
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
2
votes
4
replies
1.2k
views
I want to clarify difference between below two codes for analysis of DEGs. I got two different answers with these two methods and would like to know …
edgeR
3.5 years ago devi • 0
0
votes
1
reply
1.3k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
votes
2
replies
2.9k
views
RNA-seq: problems with edgeR installation
BiocManager edgeR
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
2
votes
17
replies
3.2k
views
How to reduce the impact of one varaible in Deseq2 or edgeR for multivariate value analysis?
MultipleComparison edgeR DESeq2
written 3.5 years ago by • 0
0
votes
0
replies
814
views
edgeR testing interactions between two factors while controlling for blocking factor
edgeR ExpressionData RNASeqData
3.5 years ago Mafalda • 0
0
votes
1
reply
6.5k
views
Why does my volcano plot look weird?
edgeR volcano_plot
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
2
votes
3
replies
1.3k
views
Classic or GLM approach in edgeR, Why do I got less DEG in GLM approach?
edgeR DEGs
updated 3.5 years ago by 53k • written 3.6 years ago by • 0
0
votes
0
replies
4.2k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
3.6 years ago Raito92 ▴ 60
15
votes
18
replies
5.0k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2 edgeR goana GO
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 60
2
votes
1
reply
1.1k
views
How to determine which model (GLM and QLF or classic edgeR) to use for DGE analysis?
edgeR
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
0
votes
1
reply
2.8k
views
Edge R Error in quantile.default(zresid, probs = prob) : missing values and NaN's not allowed if 'na.rm' is FALSE
diffSpliceDGE RNASeq DifferentialSplicingWorkflow AlternativeSplicing edgeR
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
6
votes
2
replies
946
views
The number of controls versus treatment in differential expression analysis
DESeq2 edgeR limma
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 30
1
vote
2
replies
2.1k
views
Normalize ChIP-seq samples with different signal-to-noise ratio
csaw edger tmm chipseq
updated 3.6 years ago by ★ 5.2k • written 3.6 years ago by • 0
1
vote
2
replies
1.9k
views
Gene Onotology: Can't get the goana function to work
edgeR GO
3.6 years ago Adelyn ▴ 10
2
votes
5
replies
1.9k
views
DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
1
vote
1
reply
1.2k
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
3
votes
6
replies
2.6k
views
filterbyexp() in edgeR
edgeR
updated 12 months ago by ▴ 900 • written 3.7 years ago by ▴ 10
0
votes
2
replies
1.2k
views
Extend comparisons between two groups to more groups in DESEQ2
edgeR DEGs DESEQ2 RNASeqData
3.7 years ago Raito92 ▴ 60
0
votes
6
replies
5.3k
views
Performing simple pairwise comparisons in DESEQ2
edgeR DEG RNASeq DESEQ2
updated 3.7 years ago by 43k • written 3.7 years ago by ▴ 60
2
votes
3
replies
6.0k
views
Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 3.4 years ago by • 0 • written 3.7 years ago by • 0
1
vote
4
replies
2.2k
views
Differential Splicing using edgeR
diffSpliceDGE edgeR DifferentialSplicing
3.7 years ago Assa Yeroslaviz ★ 1.5k
0
votes
3
replies
2.7k
views
using the goana function from edgeR
RNASeq edgeR GO GOSemSim
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 90
3
votes
6
replies
3.1k
views
How to use subjunc for differential splicing analysis?
subjunc edgeR
3.7 years ago Assa Yeroslaviz ★ 1.5k
2
votes
2
replies
1.3k
views
catchKallisto results are not counts
DifferentialSplicingWorkflow catchKallisto edgeR DifferentialSplicing
3.7 years ago Assa Yeroslaviz ★ 1.5k
0
votes
1
reply
1.3k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
0
votes
5
replies
1.4k
views
ANOVA-like vs direct contrast
edgeR
3.8 years ago fcamus • 0
2
votes
2
replies
5.0k
views
EdgeR installation issue
limma edgeR DESeq2
3.8 years ago aonghus • 0
3
votes
2
replies
2.1k
views
Filtering low coverage RRBS counts results in few reads. Any alternatives?
limma edgeR
updated 3.8 years ago by ▴ 10 • written 3.8 years ago by • 0
3
votes
2
replies
2.3k
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
updated 11 months ago by 53k • written 3.9 years ago by • 0
3
votes
4
replies
1.8k
views
edgeR shows different results for same dataset
edgeR
updated 3.9 years ago by 53k • written 3.9 years ago by • 0
1
vote
1
reply
2.1k
views
Help understanding edgeR code for doing exactTest
exacttest RNASeqData edgeR diffGeneAnalysis
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
2
votes
4
replies
2.0k
views
DESeq2/edgeR/limma help with most appropriate design matrix
DESeq2 limma modelmatrix edgeR designmatrix
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
2,031 results • Page 6 of 41
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Awards • All
Popular Question to Michael Love 43k
Popular Question to Peter • 0
Popular Question to Travis • 0
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Locations • All
The city by the bay, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
Iran, 3 hours ago
United States, 8 hours ago
United States, 9 hours ago
Traffic: 824 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