Showing : edger • reset
1
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59
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Citation for edgeR user guide
edgeR
updated 1 day ago by 50k • written 1 day ago by ▴ 30
4
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6
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322
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FilterByExpr low counts with small sample size
edgeR
7 days ago • updated 2 days ago Jonathan ▴ 10
0
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2
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89
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
5 days ago prity6459 • 0
0
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3
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126
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 5 days ago by 50k • written 6 days ago by • 0
3
votes
1
reply
112
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Log-cpm values from limma
limma edgeR RNASeq
updated 5 days ago by 50k • written 6 days ago by • 0
3
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3
replies
282
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permutation test in edgeR
rna-seq edgeR
updated 3 days ago by 50k • written 16 days ago by • 0
1
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3
replies
320
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 9 days ago by 50k • written 14 days ago by • 0
5
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6
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391
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 11 days ago by ★ 4.0k • written 15 days ago by ▴ 30
1
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3
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227
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 19 days ago by 65k • written 19 days ago by • 0
0
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2
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144
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
21 days ago Marianna ▴ 20
0
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4
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390
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
23 days ago • updated 22 days ago Lucy ▴ 60
3
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5
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336
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 25 days ago by 50k • written 27 days ago by • 0
0
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6
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312
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 26 days ago by 50k • written 27 days ago by • 0
0
votes
1
reply
214
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
5
votes
3
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682
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 28 days ago by 50k • written 4 weeks ago by ▴ 50
2
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3
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277
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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
0
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2
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254
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
2
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2
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242
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between lane normalization upper quantile
EDASeq edgeR
5 weeks ago elesofi • 0
2
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2
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244
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
5 weeks ago Sabiha ▴ 20
0
votes
3
replies
358
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
3
votes
4
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393
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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1
reply
210
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
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11
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699
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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
0
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1
reply
236
views
ExactTest vs QLFTest
edgeR
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
1
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6
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451
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Library size normalization in methylation count analysis
edgeR MethylationArray
8 weeks ago mico • 0
2
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6
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391
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
9 weeks ago tsl0026 • 0
5
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4
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374
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Confusion about LFC using contrasts weights in EdgeR
edgeR
9 weeks ago • updated 8 weeks ago pl23 • 0
0
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8
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603
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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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383
views
How does one test for interactions in EdgeR?
edgeR
10 weeks ago pl23 • 0
0
votes
4
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322
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Nested paired design
edgeR
11 weeks ago manduchi ▴ 10
1
vote
2
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303
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
11 weeks ago • updated 10 weeks ago mico • 0
2
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3
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350
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
4
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4
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419
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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
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7
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541
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
1
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8
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523
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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
0
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0
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231
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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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543
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
0
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3
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325
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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
votes
3
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644
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
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1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
0
votes
1
reply
294
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download problem
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
5
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595
views
Help with model for differential expression analysis
DifferentialExpression edgeR
3 months ago • updated 12 weeks ago Lucy ▴ 60
1
vote
2
replies
430
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
2
replies
530
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
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384
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
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763
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
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3
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439
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
590
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 months ago by 50k • written 5 months ago by ▴ 10
6
votes
7
replies
918
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
263
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: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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