Showing : edgeR • reset
0
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3
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1.4k
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EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
3
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3
replies
2.1k
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EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
4
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9
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2.6k
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RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
2.1 years ago • updated 2.0 years ago Luca • 0
0
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1
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647
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download problem
edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
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5
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1.5k
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Help with model for differential expression analysis
DifferentialExpression edgeR
2.1 years ago • updated 2.0 years ago Lucy ▴ 60
1
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2
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1.4k
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
2.1 years ago Sabiha ▴ 20
5
votes
2
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1.7k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
1
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2
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1.5k
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
12
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5
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5.4k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 8 months ago by • 0 • written 2.2 years ago by • 0
0
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3
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1.4k
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
2.2 years ago Karthik • 0
6
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2
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2.4k
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
6
votes
7
replies
1.9k
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by ▴ 20
0
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0
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778
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.3 years ago Florian • 0
1
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3
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952
views
edgeR: Time course RNA-seq experiments
edgeR
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
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1
reply
899
views
Batch effect adjust in model matrix
BatchEffect edgeR
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
1
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6
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3.9k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 9.2 years ago by ▴ 10
1
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4
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1.4k
views
MDS plot edgeR
edgeR
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
3
votes
3
replies
1.1k
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
1
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2
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2.1k
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Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
2.4 years ago petertam1343 • 0
1
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5
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1.4k
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 30
3
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3
replies
1.2k
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
2.4 years ago Nisha • 0
2
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3
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1.7k
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 2.5 years ago by • 0
1
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5
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1.4k
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edgeR design/contrast matrix troubles
edgeR
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
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1
reply
877
views
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 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
2
votes
4
replies
2.1k
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 2.4 years ago by 43k • written 2.5 years ago by ▴ 10
0
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0
replies
2.2k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.4 years ago Gordon Smyth 53k
2
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7
replies
5.6k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.4 years ago by • 0 • written 4.8 years ago by ▴ 20
0
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8
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3.8k
views
Question about filterByExpr function edgeR
edgeR
2.5 years ago • updated 2.4 years ago lucap • 0
0
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2
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796
views
EdgeR FTest
edgeR
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
2
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5
replies
1.9k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.5 years ago duez.tolga • 0
0
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2
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1.4k
views
EdgeR and repeated measures: how to design a correct matrix having three time points
repeatedmeasure edgeR
2.5 years ago greta • 0
1
vote
1
reply
696
views
A query about selecting the coefficient in glmLRT to test for by index
edgeR
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
0
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9
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1.5k
views
estimateDisp() error
edgeR
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
4
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3
replies
1.8k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 2.5 years ago by 53k • written 2.5 years ago by • 0
4
votes
9
replies
4.2k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
2.5 years ago Luca • 0
2
votes
5
replies
2.1k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
2.5 years ago mohammedtoufiq91 ▴ 10
6
votes
2
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1.4k
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
2.6 years ago Josué ▴ 20
1
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1
reply
1.0k
views
NA p values in edgeR results
DifferentialExpression edgeR
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
1
vote
2
replies
1.2k
views
edgeR, RRBS Library size preparation
RRBSdata edgeR methylationArrayAnalysis
2.6 years ago Krzysztof • 0
1
vote
1
reply
864
views
Best way to handle batch effects from difference Mice?
RNASeqData BatchEffect edgeR limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
3
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2
replies
1.2k
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.6 years ago by 53k • written 2.6 years ago by ▴ 30
0
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5
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1.4k
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
3
votes
6
replies
1.7k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
2
votes
1
reply
925
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
5
votes
11
replies
8.0k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 2.7 years ago by ▴ 20
5
votes
7
replies
2.4k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.0k
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
0
votes
1
reply
913
views
CI for logCPM (fitted values)
RNAseq edgeR
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
3
votes
4
replies
1.2k
views
Anova table edgeR limma
limma RNASeq edgeR
2.7 years ago KATHERINE CHUERE NUNES • 0
1
vote
2
replies
1.2k
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
2,035 results • Page 3 of 41
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Replies
Comment: msmsTests, inconsistent sign between lFC.Av and LogFC by Ben • 0
Continued here due to posting difficulties: Extract from the results table: ``` Inhibitor Vehicle lFC.Av LogFC ... F1 0.0 27…
Answer: DESeq2 for 16S rRNA Analysis by James W. MacDonald 68k
The Wald test is only meant for comparison of two groups at a time, so it depends on what you mean by 'analyze across multiple groups at a …
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Votes
A: DESeq2 - VST eliminates zero values
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
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