Showing : edger • reset
1
vote
1
reply
99
views
Citation for edgeR user guide
edgeR
updated 3 days ago by 50k • written 3 days ago by ▴ 30
4
votes
6
replies
353
views
FilterByExpr low counts with small sample size
edgeR
9 days ago • updated 4 days ago Jonathan ▴ 10
0
votes
2
replies
93
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
8 days ago prity6459 • 0
0
votes
3
replies
135
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 8 days ago by 50k • written 8 days ago by • 0
3
votes
1
reply
126
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 9 days ago by • 0
3
votes
3
replies
295
views
permutation test in edgeR
rna-seq edgeR
updated 6 days ago by 50k • written 19 days ago by • 0
1
vote
3
replies
327
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 12 days ago by 50k • written 17 days ago by • 0
5
votes
6
replies
400
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 14 days ago by ★ 4.0k • written 17 days ago by ▴ 30
1
vote
3
replies
231
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 21 days ago by 65k • written 21 days ago by • 0
0
votes
2
replies
148
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
24 days ago • updated 23 days ago Marianna ▴ 20
0
votes
4
replies
396
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
26 days ago • updated 24 days ago Lucy ▴ 60
3
votes
5
replies
347
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 27 days ago by 50k • written 29 days ago by • 0
0
votes
6
replies
324
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 28 days ago by 50k • written 29 days ago by • 0
0
votes
1
reply
220
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
votes
3
replies
694
views
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
votes
3
replies
284
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
0
votes
2
replies
260
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
2
votes
2
replies
246
views
between lane normalization upper quantile
EDASeq edgeR
6 weeks ago • updated 5 weeks ago elesofi • 0
2
votes
2
replies
250
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
1
vote
3
replies
384
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks ago by • 0
3
votes
4
replies
402
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
votes
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
11
replies
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
votes
1
reply
239
views
ExactTest vs QLFTest
edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
1
vote
6
replies
457
views
Library size normalization in methylation count analysis
edgeR MethylationArray
8 weeks ago mico • 0
2
votes
6
replies
396
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
10 weeks ago • updated 9 weeks ago tsl0026 • 0
5
votes
4
replies
380
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
10 weeks ago • updated 9 weeks ago pl23 • 0
0
votes
8
replies
609
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
10 weeks ago • updated 9 weeks ago Marianna ▴ 20
3
votes
2
replies
397
views
How does one test for interactions in EdgeR?
edgeR
11 weeks ago • updated 10 weeks ago pl23 • 0
0
votes
4
replies
328
views
Nested paired design
edgeR
11 weeks ago manduchi ▴ 10
1
vote
2
replies
310
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
11 weeks ago mico • 0
2
votes
3
replies
355
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks 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
6
votes
7
replies
552
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
1
vote
8
replies
530
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 12 weeks ago by 50k • written 3 months ago by • 0
0
votes
0
replies
236
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
556
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
0
votes
3
replies
330
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
652
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
0
votes
1
reply
298
views
download problem
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
5
replies
604
views
Help with model for differential expression analysis
DifferentialExpression edgeR
3 months ago • updated 12 weeks ago Lucy ▴ 60
1
vote
2
replies
440
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
2
replies
538
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
vote
2
replies
394
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
7
votes
2
replies
775
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
3
replies
442
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago • updated 4 months ago Karthik • 0
4
votes
2
replies
600
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
6
votes
7
replies
923
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.0k • written 6 months ago by ▴ 20
0
votes
0
replies
268
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
50 results • Page 1 of 1
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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…
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…
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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