Showing : edger • reset
1
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89
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Citation for edgeR user guide
edgeR
updated 2 days ago by 50k • written 3 days ago by ▴ 30
4
votes
6
replies
340
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FilterByExpr low counts with small sample size
edgeR
9 days ago • updated 4 days ago Jonathan ▴ 10
3
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3
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294
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permutation test in edgeR
rna-seq edgeR
updated 5 days ago by 50k • written 18 days ago by • 0
6
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10
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1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 7 days ago by • 0 • written 14 months ago by ▴ 10
0
votes
3
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133
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 7 days ago by 50k • written 8 days ago by • 0
0
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2
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91
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
7 days ago prity6459 • 0
3
votes
1
reply
122
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 8 days ago by • 0
9
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12
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7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 8 days ago by • 0 • written 8.8 years ago by ▴ 30
1
vote
3
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326
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 11 days ago by 50k • written 16 days ago by • 0
5
votes
6
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399
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 13 days ago by ★ 4.0k • written 17 days ago by ▴ 30
1
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3
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229
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 20 days ago by 65k • written 21 days ago by • 0
0
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2
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148
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
23 days ago Marianna ▴ 20
0
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4
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395
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
25 days ago • updated 24 days ago Lucy ▴ 60
0
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5
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1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 24 days ago by 50k • written 11.5 years ago by ▴ 30
3
votes
5
replies
340
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 26 days ago by 50k • written 28 days ago by • 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR edgeR
updated 27 days ago by 50k • written 12.4 years ago by ▴ 670
0
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6
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316
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 27 days ago by 50k • written 28 days ago by • 0
5
votes
3
replies
690
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 29 days ago by 50k • written 5 weeks ago by ▴ 50
0
votes
1
reply
219
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
2
votes
3
replies
280
views
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
2
votes
2
replies
245
views
between lane normalization upper quantile
EDASeq edgeR
6 weeks ago • updated 5 weeks ago elesofi • 0
0
votes
2
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259
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
2
votes
2
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248
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
1
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3
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383
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks ago by • 0
3
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4
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399
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 7 weeks ago by ▴ 50
0
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11
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702
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
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1
reply
212
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
1
reply
239
views
ExactTest vs QLFTest
edgeR
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
2
votes
5
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1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
1
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6
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456
views
Library size normalization in methylation count analysis
edgeR MethylationArray
8 weeks ago mico • 0
5
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4
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380
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
9 weeks ago pl23 • 0
0
votes
8
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607
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
10 weeks ago • updated 9 weeks ago Marianna ▴ 20
2
votes
6
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396
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
10 weeks ago • updated 9 weeks ago tsl0026 • 0
3
votes
2
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397
views
How does one test for interactions in EdgeR?
edgeR
10 weeks ago pl23 • 0
1
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2
replies
307
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
11 weeks ago mico • 0
0
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4
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327
views
Nested paired design
edgeR
11 weeks ago manduchi ▴ 10
2
votes
3
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355
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
3
votes
4
replies
8.5k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 12 weeks ago by • 0 • written 10.8 years ago by ▴ 30
1
vote
8
replies
527
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 12 weeks ago by 50k • written 3 months ago by • 0
4
votes
4
replies
421
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 12 weeks ago by 65k • written 3 months ago by • 0
0
votes
5
replies
603
views
Help with model for differential expression analysis
DifferentialExpression edgeR
3 months ago • updated 12 weeks ago Lucy ▴ 60
6
votes
7
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548
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 12 weeks ago by 50k • written 3 months ago by • 0
0
votes
0
replies
235
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
2
votes
4
replies
552
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
0
votes
3
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329
views
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
651
views
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
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
0
votes
1
reply
297
views
download problem
edgeR
updated 3 months ago by 50k • written 3 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 3 months ago by 50k • written 3.0 years ago by ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
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…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
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)
biomaRt error: database disk image is malformed
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