Showing : EdgeR • reset
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
22 months ago • updated 21 months ago Sabiha ▴ 20
5
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2
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1.5k
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 22 months ago by 53k • written 22 months ago by • 0
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2
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1.4k
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
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5
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limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by • 0 • written 22 months ago by • 0
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3
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1.2k
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
22 months ago Karthik • 0
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2
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2.1k
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 23 months ago by 53k • written 23 months ago by ▴ 10
6
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7
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1.7k
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[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 23 months ago by ★ 5.0k • written 24 months ago by ▴ 20
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701
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
24 months ago Florian • 0
1
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3
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861
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edgeR: Time course RNA-seq experiments
edgeR
updated 24 months ago by ★ 5.0k • written 2.0 years ago by • 0
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1
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821
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Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
1
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6
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3.6k
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Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 8.9 years ago by ▴ 10
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4
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1.3k
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MDS plot edgeR
edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 10
3
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3
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954
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comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
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2
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2.0k
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Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
2.1 years ago petertam1343 • 0
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5
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1.2k
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Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 30
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3
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1.1k
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EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
2.1 years ago Nisha • 0
2
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3
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1.5k
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Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 2.2 years ago by • 0
1
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5
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1.2k
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edgeR design/contrast matrix troubles
edgeR
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
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1
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813
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Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
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4
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2.0k
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Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 10
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0
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2.0k
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.1 years ago Gordon Smyth 53k
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7
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5.2k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.1 years ago by • 0 • written 4.5 years ago by ▴ 20
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8
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3.4k
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Question about filterByExpr function edgeR
edgeR
2.1 years ago lucap • 0
0
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2
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748
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EdgeR FTest
edgeR
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
2
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5
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1.7k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.2 years ago duez.tolga • 0
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2
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1.3k
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EdgeR and repeated measures: how to design a correct matrix having three time points
repeatedmeasure edgeR
2.2 years ago greta • 0
1
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1
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651
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A query about selecting the coefficient in glmLRT to test for by index
edgeR
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
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9
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1.4k
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estimateDisp() error
edgeR
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
4
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3
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1.6k
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Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
4
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9
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3.6k
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RNA seq differential expression analysis for large sample size
edgeR DESeq2
2.2 years ago Luca • 0
2
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5
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2.0k
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Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
2.2 years ago mohammedtoufiq91 ▴ 10
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2
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1.2k
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How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
2.2 years ago Josué ▴ 20
1
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1
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934
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NA p values in edgeR results
DifferentialExpression edgeR
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
1
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2
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1.1k
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edgeR, RRBS Library size preparation
RRBSdata edgeR methylationArrayAnalysis
2.3 years ago Krzysztof • 0
1
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1
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780
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Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
3
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2
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1.1k
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Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 30
0
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5
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1.4k
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Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
3
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6
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1.5k
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Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
2
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1
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858
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DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
5
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11
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7.3k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 2.4 years ago by ▴ 20
5
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7
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2.2k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
0
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1
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933
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DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
0
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1
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853
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CI for logCPM (fitted values)
RNAseq edgeR
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
3
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4
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1.1k
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Anova table edgeR limma
limma RNASeq edgeR
2.4 years ago KATHERINE CHUERE NUNES • 0
1
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2
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1.0k
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
1
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3
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1.5k
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Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
0
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1
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1.1k
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Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
2
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1
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992
views
edgeR with Successive Differences Contrast Coding?
hypothesisTesting contrastCoding edger ExperimentalDesign expressionDifferences
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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3
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1.3k
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edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
1
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1
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695
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
2,031 results • Page 3 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
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