Showing : EdgeR • reset
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High fold change reported for comparison of samples with zero values in all samples
edgeR
4.5 years ago Laura • 0
0
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1
reply
730
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Query regarding edgeR and limma
limma readDGE edgeR
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
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4
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2.0k
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Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
4.5 years ago Nirad ▴ 10
4
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5
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1.5k
views
edgeR for a mixture experiment
edgeR model-selection RRBS mixture-experiment
4.5 years ago ingerslev • 0
1
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1
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897
views
While I'm using edgeR how can I convert a .txt file and .tabular file into .RData file? please provide a code to completion of the process.
edgeR
updated 4.5 years ago by 53k • written 4.5 years ago by • 0
2
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2
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3.5k
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How do I set up a contrast matrix in edgeR with makeContrasts, when a relevant level was dropped?
edgeR RNASeq
updated 4.5 years ago by 53k • written 4.5 years ago by • 0
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3
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1.5k
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How estimateDisp, glmQLFit and glmQLFTest process my TMM normalized read count matrix?
edgeR glmQLFTest glmQLFit estimateDisp
updated 4.5 years ago by 68k • written 4.5 years ago by • 0
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2
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1.7k
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Alternative splicing analysis in edgeR: duplicate exons
edgeR Rsubread
4.6 years ago • updated 4.5 years ago jbono ▴ 10
2
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1
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1.1k
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Remove genes before normalization?
edgeR
updated 4.6 years ago by 53k • written 4.6 years ago by • 0
1
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5
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3.6k
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log2FC calculation in EdgeR
edger log2FC
written 6.0 years ago by • 0
1
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2
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1.5k
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extracting normalized counts from edgeR for using in GSEA
edgeR
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 50
0
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2
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1.7k
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Technical-biological replicates in edgeR
edgeR
updated 4.6 years ago by 53k • written 4.6 years ago by • 0
0
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2
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2.0k
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Using edgeR to analyze Cripsr/Cas9 Screening data
edger processamplicons sgrna crispr
updated 2.7 years ago by • 0 • written 7.6 years ago by ★ 1.5k
1
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7
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2.0k
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how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
4.6 years ago decppced • 0
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2
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1.3k
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time couse RNAseq experiment 2 treatments x 4 times
edgeR timecourse
4.6 years ago Lina ▴ 10
0
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2
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1.2k
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edgeR - Chapter 4.8 Time Course RNAseq experiments
edgeR TimeCourse RNASeq
updated 4.6 years ago by 53k • written 4.6 years ago by ▴ 10
0
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3
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2.0k
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add group info within DGE-object before TMM normalization
edgeR limma
updated 4.6 years ago by 53k • written 4.6 years ago by ▴ 40
0
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3
replies
3.1k
views
How to calculate coefficient of variation within group?
edgeR limma RNASeqPower
updated 3.6 years ago by 53k • written 4.6 years ago by ▴ 60
7
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12
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5.9k
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Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 2.0 years ago by • 0 • written 4.6 years ago by • 0
3
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2
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1.3k
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Why some statistically differently expressed genes are not DEGs?
RNASeqData DEGreport edgeR
4.6 years ago Wuschel ▴ 10
1
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2
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2.5k
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How can I get a list of the DE genes from edgeR?
GOanalyses edgeR DEgeneslist
updated 4.6 years ago by ▴ 900 • written 4.6 years ago by • 0
2
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8
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2.1k
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Dealing with my.contrasts with replicates containing nested samples
edgeR
4.6 years ago James • 0
3
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7
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1.9k
views
Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 4.6 years ago by 53k • written 4.6 years ago by ▴ 30
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0
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709
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interaction at any time
edgeR
4.6 years ago calvin99 ▴ 10
1
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0
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963
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Design Matrix for multiple variables in Edge R
designmatrix DifferentialExpression edgeR RNAseq
4.6 years ago nageshprabhu.k ▴ 10
2
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2
replies
1.9k
views
EDASeq normalization: genes with 0 counts
edgeR EDASeq
4.7 years ago • updated 4.4 years ago gprezza • 0
4
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8
replies
3.1k
views
Can I remove failed samples using DGEList then filterByExpr?
edgeR
4.7 years ago James • 0
2
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4
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1.4k
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edgeR design matrix for multiple factors
MutlipleFactors DesignMatrix edgeR
4.7 years ago Debayan ▴ 20
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2
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1.4k
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Help creating a paired sample design matrix in edgeR
edgeR pairedsamples designmatrix
4.7 years ago sfidemw • 0
0
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2
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1.6k
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Question: export edgeR normalised OTU table
microbiome edgeR
4.7 years ago Pozdrawiam • 0
2
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2
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2.0k
views
Calculation of logCPM in edgeR
logCPM edgeR
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 20
3
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4
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4.0k
views
Calculation of logFC in edgeR
edgeR logfc
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 20
0
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5
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1.7k
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edgeR model matrix with 3 factors and interactions
interactionterm edgeR modelmatrix
4.7 years ago ahsindoomilup • 0
0
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2
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1.1k
views
Design Matrix for DESeq2 or EdgeR
edgeR DESeq2 RNASeq
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
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3
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1.3k
views
Question regarding lib.sizes when using glmQLFit
glmQLFit edgeR
updated 4.8 years ago by 53k • written 4.8 years ago by ▴ 170
1
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1
reply
999
views
Accounting for fish body mass in DE?
GeneExpression edgeR
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
0
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2
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1.3k
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Differential expression on RNAseq without replicates
DESeq2 NOISeq edgeR
updated 4.8 years ago by ★ 5.0k • written 4.8 years ago by • 0
1
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1
reply
856
views
Additive Model for Variable Adjustment in edgeR
edgeR
updated 4.8 years ago by ▴ 900 • written 4.8 years ago by • 0
2
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2
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1.4k
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Addressing the batch effect in multifactor experiment
edgeR BatchEffect RNASeq
updated 4.9 years ago by ▴ 360 • written 4.9 years ago by ▴ 10
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2
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2.0k
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How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
4.9 years ago harelarik ▴ 60
1
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5
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1.7k
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Is edgeR suitable for differential abundance of UNIref features from metatranscriptomics from HUMANnN2?
edgeR HUMAnN2.0
4.9 years ago Nick • 0
1
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2
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1.5k
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Roast (fry) gene set testing with offset
EDASeq edgeR limma
4.9 years ago gprezza • 0
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0
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1.1k
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tissue specific differential expression using edgeR -- accounting for other effects in the model
edgeR DifferentialExpression
4.9 years ago Christy • 0
0
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3
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3.1k
views
Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 4.9 years ago by 53k • written 4.9 years ago by ▴ 10
2
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3
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2.9k
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Normalization for within-sample gene correlation
edgeR Normalization DESeq2 tpm RNASeq
updated 4.9 years ago by 53k • written 4.9 years ago by ▴ 100
2
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2
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2.0k
views
Treatment AND Sex in EdgeR
edgeR
updated 4.9 years ago by ★ 13k • written 4.9 years ago by • 0
5
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4
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2.7k
views
edgeR supports continuous covariates?
edgeR
updated 2.7 years ago by • 0 • written 4.9 years ago by • 0
0
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3
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2.1k
views
edgeR::filterByExpr() returns unexpected result
edgeR
updated 4.9 years ago by 53k • written 5.0 years ago by • 0
4
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3
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3.6k
views
EdgeR analysis with no replicates - how to run exact test with set dispersion value?
edgeR
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
0
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3
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2.1k
views
Offsets and normalization in EdgeR
edgeR DifferentialExpression
updated 4.9 years ago by 53k • written 4.9 years ago by • 0
2,031 results • Page 8 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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