Showing : EDGER • reset
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
22 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 23 months ago by 53k • written 23 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 23 months ago by 53k • written 23 months ago by • 0
12
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5
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5.0k
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limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by • 0 • written 23 months ago by • 0
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
23 months ago Karthik • 0
5
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2
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2.2k
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 2.0 years ago by 53k • written 2.0 years 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 2.0 years ago by ★ 5.0k • written 2.0 years ago by ▴ 20
0
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0
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713
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.0 years ago Florian • 0
1
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3
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883
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edgeR: Time course RNA-seq experiments
edgeR
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by • 0
0
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1
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836
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Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.1 years ago by ★ 5.0k • written 2.1 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 9.0 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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977
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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
1
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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
1
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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
3
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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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1.3k
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edgeR design/contrast matrix troubles
edgeR
updated 2.1 years ago by 68k • written 2.2 years ago by • 0
0
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1
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829
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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 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
2
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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 2.2 years ago by 43k • written 2.2 years ago by ▴ 10
0
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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
2.2 years ago Gordon Smyth 53k
2
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7
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5.2k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.2 years ago by • 0 • written 4.5 years ago by ▴ 20
0
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8
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3.5k
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Question about filterByExpr function edgeR
edgeR
2.2 years ago lucap • 0
0
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2
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761
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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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1.8k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.2 years ago duez.tolga • 0
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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662
views
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
0
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9
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1.5k
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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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1.7k
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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
2.3 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
2.3 years ago mohammedtoufiq91 ▴ 10
6
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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
2.3 years ago Josué ▴ 20
1
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1
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947
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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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796
views
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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1.2k
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.4 years ago by 53k • written 2.4 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 2.4 years ago by 68k • written 2.4 years ago by • 0
3
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6
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1.5k
views
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
reply
874
views
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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7.4k
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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
views
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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948
views
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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869
views
CI for logCPM (fitted values)
RNAseq edgeR
updated 2.5 years ago by 53k • written 2.5 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
2.5 years ago KATHERINE CHUERE NUNES • 0
1
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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 2.5 years ago by 53k • written 2.5 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 2.5 years ago by 53k • written 2.5 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 2.5 years ago by 53k • written 2.5 years ago by • 0
2
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1
reply
1.0k
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
reply
711
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: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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