Showing : EdgeR • reset
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
24 months ago • updated 23 months ago Sabiha ▴ 20
5
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2
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1.6k
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
12
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5
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limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 6 months ago by • 0 • written 2.0 years ago by • 0
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3
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1.3k
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
2.0 years ago Karthik • 0
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2
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2.2k
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 10
6
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7
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1.8k
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[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by ▴ 20
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0
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737
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.1 years ago Florian • 0
1
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3
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909
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edgeR: Time course RNA-seq experiments
edgeR
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
0
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1
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863
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Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
1
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6
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3.7k
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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 9.1 years ago by ▴ 10
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4
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1.3k
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MDS plot edgeR
edgeR
updated 2.2 years ago by 53k • written 2.2 years ago by ▴ 10
3
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3
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1.0k
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comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
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2.0k
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Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
2.2 years ago petertam1343 • 0
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5
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1.3k
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Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 2.2 years ago by 53k • written 2.2 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
2.2 years ago Nisha • 0
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3
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1.6k
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Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 2.3 years ago by • 0
1
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5
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1.3k
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edgeR design/contrast matrix troubles
edgeR
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
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858
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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 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
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4
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2.1k
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Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 10
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0
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2.1k
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.3 years ago Gordon Smyth 53k
2
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7
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5.3k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.3 years ago by • 0 • written 4.6 years ago by ▴ 20
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8
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3.5k
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Question about filterByExpr function edgeR
edgeR
2.3 years ago lucap • 0
0
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2
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777
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EdgeR FTest
edgeR
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
2
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5
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1.8k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.3 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
2.3 years ago greta • 0
1
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1
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674
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A query about selecting the coefficient in glmLRT to test for by index
edgeR
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
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9
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1.5k
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estimateDisp() error
edgeR
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
4
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3
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1.7k
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Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
4
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9
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3.7k
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RNA seq differential expression analysis for large sample size
edgeR DESeq2
2.4 years ago Luca • 0
2
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5
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2.1k
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Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
2.4 years ago mohammedtoufiq91 ▴ 10
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2
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1.3k
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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
2.4 years ago Josué ▴ 20
1
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1
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969
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NA p values in edgeR results
DifferentialExpression edgeR
updated 2.4 years ago by 53k • written 2.4 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
2.4 years ago Krzysztof • 0
1
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1
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823
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Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
3
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2
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1.2k
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Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.5 years ago by 53k • written 2.5 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 2.5 years ago by 68k • written 2.5 years ago by • 0
3
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6
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1.6k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
2
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1
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892
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DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
5
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11
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7.5k
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Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 2.5 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 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
0
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1
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980
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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 2.5 years ago by ★ 1.4k • written 2.6 years ago by • 0
0
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1
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882
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CI for logCPM (fitted values)
RNAseq edgeR
updated 2.6 years ago by 53k • written 2.6 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
2.6 years ago KATHERINE CHUERE NUNES • 0
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2
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1.1k
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
1
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3
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1.6k
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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 2.6 years ago by 53k • written 2.6 years ago by • 0
0
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1.1k
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Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
2
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1
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1.0k
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edgeR with Successive Differences Contrast Coding?
hypothesisTesting contrastCoding edger ExperimentalDesign expressionDifferences
updated 2.6 years ago by 53k • written 2.6 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 2.6 years ago by 53k • written 2.6 years ago by • 0
1
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1
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729
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
2,031 results • Page 3 of 41
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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Popular Question to James W. MacDonald 68k
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