Showing : edgeR • reset
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 8 hours ago by 50k • written 10 hours ago by • 0
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1
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159
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 11 days ago by 50k • written 11 days ago by • 0
4
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2
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601
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
11 days ago • updated 7 days ago gene_bioconductor ▴ 10
1
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1
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188
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Citation for edgeR user guide
edgeR
updated 20 days ago by 50k • written 20 days ago by ▴ 30
4
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6
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450
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FilterByExpr low counts with small sample size
edgeR
26 days ago • updated 21 days ago Jonathan ▴ 10
0
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2
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143
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
25 days ago • updated 24 days ago prity6459 • 0
0
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3
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202
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 24 days ago by 50k • written 25 days ago by • 0
5
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3
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289
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Log-cpm values from limma
limma edgeR RNASeq
updated 4 days ago by 50k • written 26 days ago by • 0
3
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3
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359
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permutation test in edgeR
rna-seq edgeR
updated 23 days ago by 50k • written 5 weeks ago by • 0
1
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3
replies
359
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 28 days ago by 50k • written 4 weeks ago by • 0
5
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6
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446
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by ▴ 30
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3
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273
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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
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2
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185
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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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442
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 weeks ago • updated 5 weeks ago Lucy ▴ 60
3
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5
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402
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
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6
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366
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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
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1
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246
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
5
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3
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727
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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
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3
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302
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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2
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296
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
2
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2
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267
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between lane normalization upper quantile
EDASeq edgeR
8 weeks ago elesofi • 0
2
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2
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277
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
1
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3
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431
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
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4
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470
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 weeks ago by 50k • written 10 weeks ago by ▴ 50
0
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1
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230
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
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11
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763
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
0
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1
reply
272
views
ExactTest vs QLFTest
edgeR
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
1
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6
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517
views
Library size normalization in methylation count analysis
edgeR MethylationArray
11 weeks ago mico • 0
2
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6
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431
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
12 weeks ago tsl0026 • 0
5
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4
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414
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
12 weeks ago • updated 11 weeks ago pl23 • 0
0
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8
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671
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 11 weeks ago Marianna ▴ 20
3
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2
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477
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How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
0
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4
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361
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
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2
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336
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
2
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3
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382
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
4
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4
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447
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edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 4 months ago by • 0
6
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7
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590
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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559
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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257
views
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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617
views
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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356
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
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3
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695
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
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9
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1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago • updated 3 months ago Luca • 0
0
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1
reply
317
views
download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
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5
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634
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
vote
2
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484
views
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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590
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
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445
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
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834
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
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3
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470
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: ChAMP installation issue by e1271094 • 0
I discovered that the dataset data("probe.features.epicv1") is unavailable. Instead, the dataset data("probe.features.epic") is accessible.…
Comment: ChAMP installation issue by e1271094 • 0
I apologise for any inconvenience. I have successfully installed the ChAMP package. However, I am now encountering a new error: myLoad <- …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Yes, blockLength=200000, and seg=seg. I am concerned about the inter-feature distance of features. I generated this plot for various bloc…
Answer: Can I trust the differential expression analysis when the two groups overlap on by Michael Love 42k
Can you use `vst` instead of `rlog` and increase to 1000 or 2000 genes? I'm wondering if there's a way to characterize these 7 samples. …
Comment: Can I trust the differential expression analysis when the two groups overlap on by BioinfGuru ▴ 30
I think I am about to run into the same issue with my data, so I'll be interested to read peoples opinions on this also i.e. when the group…
Votes
Answer: Error EPICv2 ChAMP
Comment: Store output of matchPWM()
Answer: Store output of matchPWM()
Answer: Store output of matchPWM()
Answer: ChipQC 'names' attribute [9] must be the same length as the vector [2]'
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