Showing : edgeR • reset
1
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6
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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 7.5 years ago by ▴ 10
2
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3
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804
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Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
2
votes
7
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2.9k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
9
votes
5
replies
5.1k
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Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
1
vote
5
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675
views
edgeR design/contrast matrix troubles
edgeR
updated 7 months ago by 65k • written 7 months ago by • 0
0
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9
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845
views
estimateDisp() error
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
5
votes
2
replies
547
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
1
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4
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727
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MDS plot edgeR
edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 10
0
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2
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264
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
4
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9
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1.3k
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RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
5
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9
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2.5k
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edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 8 months ago by • 0 • written 6.4 years ago by ▴ 10
0
votes
6
replies
348
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
6
votes
7
replies
941
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 6 months ago by ▴ 20
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago mohammedtoufiq91 ▴ 10
4
votes
7
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13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 22 months ago by ▴ 30
0
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3
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452
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
3
votes
3
replies
314
views
permutation test in edgeR
rna-seq edgeR
updated 11 days ago by 50k • written 24 days ago by • 0
4
votes
4
replies
430
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 3 months ago by • 0
2
votes
8
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2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
12 months ago • updated 11 months ago Luis • 0
1
vote
3
replies
342
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 17 days ago by 50k • written 22 days ago by • 0
9
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12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 13 days ago by • 0 • written 8.8 years ago by ▴ 30
3
votes
4
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8.6k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.8 years ago by ▴ 30
1
vote
5
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846
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
0
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4
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875
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 41k • written 8 months ago by • 0
1
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3
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394
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
0
votes
2
replies
474
views
EdgeR FTest
edgeR
updated 8 months ago by 50k • written 8 months ago by • 0
1
vote
2
replies
408
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
1
vote
2
replies
641
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 11 months ago by 50k • written 11 months ago by • 0
0
votes
3
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336
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EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
3
replies
542
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
7 months ago Nisha • 0
3
votes
1
reply
158
views
Log-cpm values from limma
limma edgeR RNASeq
updated 13 days ago by 50k • written 14 days ago by • 0
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 7 months ago by • 0 • written 3.2 years ago by • 0
1
vote
1
reply
399
views
A query about selecting the coefficient in glmLRT to test for by index
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
1
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5
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732
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 30
4
votes
3
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1.8k
views
catchSalmon for tx-level DE
catchSalmon edgeR
updated 5 months ago by 50k • written 3.5 years ago by ★ 4.1k
4
votes
6
replies
397
views
FilterByExpr low counts with small sample size
edgeR
14 days ago • updated 9 days ago Jonathan ▴ 10
0
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2
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1.1k
views
library size and fold changes
edgeR edgeR
updated 4 weeks ago by 50k • written 12.4 years ago by ▴ 670
1
vote
2
replies
452
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
1
vote
3
replies
796
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 12 months ago by 50k • written 12 months ago by • 0
0
votes
1
reply
231
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
1
reply
497
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 8 months ago by ★ 4.1k • written 8 months ago by • 0
2
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3
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363
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
2
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6
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403
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
10 weeks ago tsl0026 • 0
2
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2
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2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 8 months ago by • 0 • written 6.4 years ago by • 0
2
votes
1
reply
601
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
2
votes
4
replies
579
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
0
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2
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121
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
13 days ago prity6459 • 0
0
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11
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2.8k
views
edgeR contrasts
edgeR
updated 8 months ago by 65k • written 19 months ago by • 0
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.0 years ago by ▴ 60
7
votes
2
replies
797
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Postdoctoral Position in Bioinformatics - Mainz, Germany by Jammie • 0
[Online kasiinod][1] pakuvad mängijatele võimalust nautida põnevat hasartmängukogemust otse oma arvuti või mobiilseadme kaudu. Need kasiino…
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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