Showing : EdgeR • reset
0
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5
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2.4k
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RNA-seq with patient samples without replicates with multiple timepoints
edgeR RNASeq multi
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
2
votes
1
reply
2.6k
views
How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?
DESeq2 tximport Kallisto TMM edgeR
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
2
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3
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1.3k
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edgeR contrasts confusion when multiple groups are involved
edgeR
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
7
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12
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6.2k
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.fastq to .txt conversion for EdgeR package and merging two paired end sequence files
EdgeR normalization fastq txt TMM
updated 3.4 years ago by 53k • written 9.9 years ago by • 0
0
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2
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1.3k
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How to convert TMM RNA-seq file (generated by edgeR) to list of differentially expressed genes
edgeR DifferentialExpression TMM RNASeq
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
0
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0
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1.0k
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MEDIPS.meth output
MEDIPS edgeR l
4.1 years ago Aranzazu • 0
0
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7
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2.6k
views
Returning to edgeR version 3.26.1?
edgeR Bioconductor
updated 4.1 years ago by 53k • written 4.1 years ago by • 0
2
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7
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2.1k
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EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on individual patients not combined
edgeR StatisticalMethod
4.1 years ago Field -Ye • 0
2
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3
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1.4k
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Repeated tag sequence error
edgeR
updated 4.1 years ago by 53k • written 4.1 years ago by • 0
0
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2
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1.5k
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Gene expression in R
limma edgeR Biobase GeneExpression
4.1 years ago sogol.bouyeh • 0
3
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5
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7.6k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
4.1 years ago zhxiaokang ▴ 20
5
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7
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2.3k
views
Nanostringdiff - defining contrast values for blocking variables in glm
limma edgeR DESeq2 NanoStringDiff
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
1
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2
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1.4k
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Results Goana after edgeR pipeline
EdgeR Bioinformatics Goana
4.1 years ago Barista • 0
1
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2
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1.9k
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Not many DE genes using glmTreat
EdgeR Bioinformatics Transcriptomics Quantseq
4.1 years ago Barista • 0
0
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2
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1.2k
views
catchSalmon
catchSalmon edgeR
updated 2.5 years ago by 53k • written 4.2 years ago by ▴ 620
0
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2
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2.2k
views
same padj for all the genes after DEseq analysis
etLRT WALD edgeR DESEq
updated 4.2 years ago by 43k • written 4.2 years ago by • 0
1
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5
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1.7k
views
makeContrasts question
makeContrasts edgeR
updated 4.2 years ago by ★ 13k • written 4.2 years ago by ▴ 10
2
votes
4
replies
1.9k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
4.2 years ago mbenegas ▴ 10
0
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3
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1.4k
views
EdgeR question: why I got discrepancy results for DEGs when using different ways setting up the models
RNAseq edgeR DEGs
updated 3.6 years ago by 53k • written 4.2 years ago by ▴ 380
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3
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2.1k
views
Why does "robust=TRUE" not work as a third argument in estimateDisp of edgeR 3.34.0?
edgeR
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
0
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2
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1.8k
views
Using both spike in and TMM normalizations in ChIP-seq samples
ChIPSeq SpikeIn edgeR Normalization
4.2 years ago maria.soler • 0
5
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9
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2.3k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 4.2 years ago by 68k • written 4.2 years ago by ▴ 840
3
votes
4
replies
5.8k
views
differential expression for Single-cell RNAseq data using edgeR
edgeR single scRNAseq
4.2 years ago • updated 4.1 years ago mbenegas ▴ 10
0
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3
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1.3k
views
edgeR
edgeR DifferentialExpression
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
1
vote
1
reply
1.8k
views
Repeated measures RNAseq analysis (edgeR or limma-voom)
edgeR limma variancePartition
updated 4.2 years ago by 53k • written 4.2 years ago by • 0
1
vote
3
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1.2k
views
subset a list based on table
edgeR RNASeq resfilt
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by • 0
2
votes
9
replies
3.3k
views
extract fold change of a list of gene from EdgeR?
EdgeR RNAseq Foldchange
updated 4.3 years ago by ★ 1.4k • written 4.3 years ago by • 0
4
votes
7
replies
2.2k
views
Spline-fitted data analysis in edgeR question
edgeR
4.3 years ago erik.burchard • 0
1
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1
reply
1.2k
views
DiffBind normalisation factor retrieval
edgeR Normalization DiffBind
updated 4.3 years ago by ★ 5.2k • written 4.3 years ago by • 0
2
votes
1
reply
1.4k
views
Complex design with paired and unpaired samples with edgeR RNA-seq DE analysis
edgeR RNASeq
updated 4.3 years ago by 53k • written 4.3 years ago by ▴ 780
4
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8
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3.1k
views
change text size in plotmd functtion
edgeR plotmd
4.3 years ago najib • 0
8
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3
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7.1k
views
edgeR calcNormFactors or normalization factors with voom?
edgeR limma
4.3 years ago XTR5 ▴ 10
0
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1
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730
views
Creating the correct model to account for paired-samples (patient-effect) help needed!
edgeR limma rnaseq
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
1
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1
reply
1.3k
views
DESeq2 for allele-specific expression with contrasts between conditions
DESeq2 AllelicImbalance edgeR RNASeq
updated 4.3 years ago by 43k • written 4.3 years ago by • 0
4
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5
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2.0k
views
No counts, just fold change data
EdgeR Estimation Dispersion
4.3 years ago Manal • 0
2
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3
replies
1.3k
views
Confusion using edgeR and spline-fitted data
edgeR
updated 4.3 years ago by 53k • written 4.3 years ago by • 0
1
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6
replies
2.3k
views
Differential Transcript Usage: complex factorial design
edgeR DEXSeq IsoformSwitchAnalyzeR DTU
updated 4.3 years ago by ▴ 120 • written 4.5 years ago by ▴ 10
1
vote
1
reply
837
views
Continuous variable that differs between repetitions and treatments DE Analysis in edgeR
edgeR
updated 4.3 years ago by 53k • written 4.3 years ago by • 0
0
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3
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1.9k
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[DEseq2] How to properly add a noise coefficient to the experiment design formula
limma edgeR DEseq2
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 30
2
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3
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1.8k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 4.4 years ago by 53k • written 4.4 years ago by • 0
0
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1
reply
1.7k
views
edgeR on microRNA data
miRNA edgeR miRNA edgeR
updated 4.4 years ago by 53k • written 14.0 years ago by ▴ 50
4
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3
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2.0k
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 40
1
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1
reply
2.3k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 4.4 years ago by ★ 1.1k • written 4.4 years ago by ▴ 20
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0
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606
views
Building contrasts in edgeR with hierarchical and unbalanced experiment design
edgeR
4.4 years ago David • 0
1
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1
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1.3k
views
Optimal edgeR design for a single-factor experiment
factors edgeR setup DGELIst
updated 4.4 years ago by 53k • written 4.4 years ago by • 0
7
votes
3
replies
2.1k
views
Effect of feature number on adjusted p-values
edgeR DESeq2 single-cell scRNAseq zinbwave
updated 4.4 years ago by ★ 29k • written 4.4 years ago by ▴ 20
1
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1
reply
1.0k
views
edgeR & blocking with complex experimental design
edgeR blocking
updated 4.4 years ago by ▴ 900 • written 4.4 years ago by • 0
4
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1
reply
3.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 21 months ago by 53k • written 4.4 years ago by ▴ 60
0
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4
replies
1.6k
views
subtracting or normalizing RNAseq reads when samples have contaminating reads
Normalization RNASeq contamination edgeR DESeq2
4.5 years ago Yuqia • 0
3
votes
4
replies
1.9k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
4.5 years ago Antonio M. • 0
2,031 results • Page 7 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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