Showing : edgeR • reset
4
votes
2
replies
584
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
8 days ago • updated 5 days ago gene_bioconductor ▴ 10
0
votes
1
reply
145
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 8 days ago by 50k • written 8 days ago by • 0
1
vote
1
reply
184
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Citation for edgeR user guide
edgeR
updated 17 days ago by 50k • written 17 days ago by ▴ 30
0
votes
2
replies
142
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
22 days ago prity6459 • 0
0
votes
3
replies
195
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 22 days ago by 50k • written 23 days ago by • 0
5
votes
3
replies
271
views
Log-cpm values from limma
limma edgeR RNASeq
updated 1 day ago by 50k • written 23 days ago by • 0
4
votes
6
replies
448
views
FilterByExpr low counts with small sample size
edgeR
24 days ago • updated 19 days ago Jonathan ▴ 10
1
vote
3
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356
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 26 days ago by 50k • written 4 weeks ago by • 0
5
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6
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444
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 28 days ago by ★ 4.1k • written 4 weeks ago by ▴ 30
3
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3
replies
355
views
permutation test in edgeR
rna-seq edgeR
updated 20 days ago by 50k • written 4 weeks ago by • 0
1
vote
3
replies
269
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
0
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2
replies
184
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
5 weeks ago Marianna ▴ 20
0
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4
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441
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
5 weeks ago Lucy ▴ 60
3
votes
5
replies
398
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
6
replies
365
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
1
reply
241
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
5
votes
3
replies
727
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 50
2
votes
3
replies
301
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
2
replies
294
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
2
votes
2
replies
264
views
between lane normalization upper quantile
EDASeq edgeR
8 weeks ago • updated 7 weeks ago elesofi • 0
2
votes
2
replies
273
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
3
votes
4
replies
456
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by ▴ 50
0
votes
1
reply
227
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
votes
1
reply
267
views
ExactTest vs QLFTest
edgeR
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
0
votes
11
replies
759
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 9 weeks ago by 50k • written 10 weeks ago by • 0
1
vote
6
replies
510
views
Library size normalization in methylation count analysis
edgeR MethylationArray
10 weeks ago mico • 0
5
votes
4
replies
409
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
12 weeks ago • updated 11 weeks ago pl23 • 0
2
votes
6
replies
424
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
12 weeks ago • updated 11 weeks ago tsl0026 • 0
0
votes
8
replies
656
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
12 weeks ago • updated 11 weeks ago Marianna ▴ 20
3
votes
2
replies
460
views
How does one test for interactions in EdgeR?
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
0
votes
4
replies
356
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
vote
2
replies
334
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
2
votes
3
replies
378
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
1
vote
3
replies
425
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
6
votes
7
replies
585
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
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8
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555
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
0
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0
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255
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
2
votes
4
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610
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
352
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
691
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
4
replies
441
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 4 months ago by • 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago • updated 3 months ago Luca • 0
0
votes
1
reply
315
views
download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
5
replies
629
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
vote
2
replies
480
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
2
replies
585
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
1
vote
2
replies
440
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
7
votes
2
replies
827
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
votes
3
replies
467
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
4
votes
2
replies
650
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
50 results • Page 1 of 1
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Answer: SingleR Label.Ont by Denis • 0
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Comment: deseq2 results by sajadahmad41454 • 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
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