Showing : edger • reset
1
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146
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Citation for edgeR user guide
edgeR
updated 6 days ago by 50k • written 7 days ago by ▴ 30
0
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2
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114
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
11 days ago prity6459 • 0
0
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3
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161
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 11 days ago by 50k • written 12 days ago by • 0
3
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1
reply
150
views
Log-cpm values from limma
limma edgeR RNASeq
updated 11 days ago by 50k • written 12 days ago by • 0
4
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6
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381
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FilterByExpr low counts with small sample size
edgeR
13 days ago • updated 8 days ago Jonathan ▴ 10
1
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3
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335
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 15 days ago by 50k • written 20 days ago by • 0
5
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6
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408
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 17 days ago by ★ 4.1k • written 21 days ago by ▴ 30
3
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3
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309
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permutation test in edgeR
rna-seq edgeR
updated 9 days ago by 50k • written 22 days ago by • 0
1
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3
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237
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 24 days ago by 65k • written 25 days ago by • 0
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2
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152
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
27 days ago Marianna ▴ 20
0
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4
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403
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
29 days ago • updated 28 days ago Lucy ▴ 60
3
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5
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366
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
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6
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337
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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
0
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1
reply
225
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
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3
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700
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 4 weeks ago by 50k • written 5 weeks ago by ▴ 50
2
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3
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284
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
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2
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260
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
2
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2
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249
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between lane normalization upper quantile
EDASeq edgeR
6 weeks ago elesofi • 0
2
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2
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251
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
3
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4
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412
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
0
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1
reply
214
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Different results from DGE using different subgroups in model.matrix
edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
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1
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242
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ExactTest vs QLFTest
edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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11
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711
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
1
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6
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469
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Library size normalization in methylation count analysis
edgeR MethylationArray
9 weeks ago mico • 0
5
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4
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383
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Confusion about LFC using contrasts weights in EdgeR
edgeR
10 weeks ago • updated 9 weeks ago pl23 • 0
2
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6
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402
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
10 weeks ago tsl0026 • 0
0
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8
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618
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
11 weeks ago • updated 10 weeks ago Marianna ▴ 20
3
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2
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408
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How does one test for interactions in EdgeR?
edgeR
11 weeks ago pl23 • 0
0
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4
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339
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Nested paired design
edgeR
11 weeks ago manduchi ▴ 10
1
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2
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318
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
11 weeks ago mico • 0
2
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3
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358
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
1
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3
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386
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks ago by • 0
6
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7
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558
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readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
1
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8
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533
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
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0
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240
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
2
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4
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569
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
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3
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333
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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
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3
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657
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EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
4
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4
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427
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edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 3 months ago by • 0
4
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9
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1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
0
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1
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301
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download problem
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
0
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5
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607
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
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2
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445
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
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2
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544
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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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2
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401
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
7
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2
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781
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
0
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3
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448
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
4
votes
2
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610
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
0
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0
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272
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
6
votes
7
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934
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 6 months ago by ▴ 20
50 results • Page 1 of 1
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Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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