Showing : edgeR • reset
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Citation for edgeR user guide
edgeR
updated 4 days ago by 50k • written 4 days ago by ▴ 30
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2
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103
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
9 days ago prity6459 • 0
0
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3
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147
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 9 days ago by 50k • written 10 days ago by • 0
3
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1
reply
137
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Log-cpm values from limma
limma edgeR RNASeq
updated 9 days ago by 50k • written 10 days ago by • 0
4
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6
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364
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FilterByExpr low counts with small sample size
edgeR
11 days ago • updated 6 days ago Jonathan ▴ 10
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3
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329
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 13 days ago by 50k • written 18 days ago by • 0
5
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6
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401
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 15 days ago by ★ 4.0k • written 19 days ago by ▴ 30
3
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3
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295
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permutation test in edgeR
rna-seq edgeR
updated 7 days ago by 50k • written 20 days ago by • 0
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3
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233
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 22 days ago by 65k • written 23 days ago by • 0
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2
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150
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
25 days ago Marianna ▴ 20
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4
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398
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
27 days ago • updated 26 days ago Lucy ▴ 60
3
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5
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356
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 28 days ago by 50k • written 4 weeks ago by • 0
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6
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331
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 29 days ago by 50k • written 4 weeks ago by • 0
0
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1
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221
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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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695
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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
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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 5 weeks ago by 50k • written 5 weeks ago by • 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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248
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between lane normalization upper quantile
EDASeq edgeR
6 weeks ago • updated 5 weeks ago elesofi • 0
2
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2
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250
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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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404
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 7 weeks ago by ▴ 50
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1
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213
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Different results from DGE using different subgroups in model.matrix
edgeR
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
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1
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241
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ExactTest vs QLFTest
edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
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11
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705
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
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6
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461
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Library size normalization in methylation count analysis
edgeR MethylationArray
8 weeks ago mico • 0
5
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4
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381
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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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399
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
10 weeks ago • updated 9 weeks ago tsl0026 • 0
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8
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615
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
10 weeks ago • updated 9 weeks ago Marianna ▴ 20
3
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2
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401
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How does one test for interactions in EdgeR?
edgeR
11 weeks ago • updated 10 weeks ago pl23 • 0
0
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4
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330
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Nested paired design
edgeR
11 weeks ago manduchi ▴ 10
1
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2
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311
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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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355
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
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3
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384
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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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556
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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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532
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 12 weeks ago by 50k • written 3 months ago by • 0
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237
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
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4
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557
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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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331
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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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653
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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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422
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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
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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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300
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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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606
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Help with model for differential expression analysis
DifferentialExpression edgeR
3 months ago Lucy ▴ 60
1
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2
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442
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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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540
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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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396
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
7
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2
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776
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limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 5 months ago by • 0
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3
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446
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
4
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2
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603
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
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0
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269
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
6
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7
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925
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[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.0k • written 6 months ago by ▴ 20
50 results • Page 1 of 1
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Replies
Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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