Showing : edgeR • reset
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 9 days ago by 50k • written 9 days ago by • 0
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585
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
9 days ago • updated 5 days ago gene_bioconductor ▴ 10
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184
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Citation for edgeR user guide
edgeR
updated 18 days ago by 50k • written 18 days ago by ▴ 30
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6
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448
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FilterByExpr low counts with small sample size
edgeR
24 days ago • updated 19 days ago Jonathan ▴ 10
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142
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
22 days ago prity6459 • 0
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3
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196
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 22 days ago by 50k • written 23 days ago by • 0
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3
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274
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Log-cpm values from limma
limma edgeR RNASeq
updated 1 day ago by 50k • written 23 days ago by • 0
3
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3
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355
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permutation test in edgeR
rna-seq edgeR
updated 20 days ago by 50k • written 4 weeks ago by • 0
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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
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6
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445
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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
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3
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269
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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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184
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
5 weeks ago Marianna ▴ 20
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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
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5
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398
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
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6
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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
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1
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241
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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
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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
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3
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301
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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
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2
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294
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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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264
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between lane normalization upper quantile
EDASeq edgeR
8 weeks ago • updated 7 weeks ago elesofi • 0
2
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2
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273
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
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3
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426
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
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4
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457
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by ▴ 50
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227
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Different results from DGE using different subgroups in model.matrix
edgeR
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
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11
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759
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 9 weeks ago by 50k • written 10 weeks ago by • 0
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1
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267
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ExactTest vs QLFTest
edgeR
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
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6
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511
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Library size normalization in methylation count analysis
edgeR MethylationArray
10 weeks ago mico • 0
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6
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424
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
12 weeks ago • updated 11 weeks ago tsl0026 • 0
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4
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409
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Confusion about LFC using contrasts weights in EdgeR
edgeR
12 weeks ago • updated 11 weeks ago pl23 • 0
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8
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656
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
12 weeks ago • updated 11 weeks ago Marianna ▴ 20
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461
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How does one test for interactions in EdgeR?
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
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4
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356
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Nested paired design
edgeR
3 months ago manduchi ▴ 10
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334
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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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378
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
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4
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441
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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
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585
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readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
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8
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556
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
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256
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
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4
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611
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
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3
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352
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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
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3
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691
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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
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9
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1.1k
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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
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315
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download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
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5
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629
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
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2
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480
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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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585
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Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
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2
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442
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
7
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2
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828
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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
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3
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467
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
4
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2
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652
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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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Comment: More regions in union when increasing DBA$config$mergeOverlap by Ziliang • 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
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
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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