Showing : edgeR • reset
2
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3
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115
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 2 days ago by 50k • written 3 days ago by • 0
1
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3
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235
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 3 days ago by 50k • written 4 days ago by • 0
0
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1
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172
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 15 days ago by 50k • written 15 days ago by • 0
4
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2
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620
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
15 days ago • updated 11 days ago gene_bioconductor ▴ 10
1
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2
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203
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Citation for edgeR user guide
edgeR
written 24 days ago by ▴ 30
4
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6
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469
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FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 25 days ago Jonathan ▴ 10
0
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2
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147
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
29 days ago prity6459 • 0
0
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3
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210
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 29 days ago by 50k • written 29 days ago by • 0
5
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3
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305
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Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 4 weeks ago by • 0
3
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3
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368
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permutation test in edgeR
rna-seq edgeR
updated 27 days ago by 50k • written 5 weeks ago by • 0
1
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3
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368
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
5
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6
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456
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
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3
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279
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
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2
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196
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
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4
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447
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 weeks ago Lucy ▴ 60
3
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5
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412
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
0
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6
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370
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
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1
reply
250
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
5
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3
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735
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
2
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3
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310
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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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305
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
2
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2
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274
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between lane normalization upper quantile
EDASeq edgeR
9 weeks ago • updated 8 weeks ago elesofi • 0
2
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2
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289
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
1
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3
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439
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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508
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 50
0
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1
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241
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Different results from DGE using different subgroups in model.matrix
edgeR
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
0
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11
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789
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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
283
views
ExactTest vs QLFTest
edgeR
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
1
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6
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528
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Library size normalization in methylation count analysis
edgeR MethylationArray
11 weeks ago mico • 0
2
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6
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438
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago • updated 12 weeks ago tsl0026 • 0
5
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4
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429
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Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
0
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8
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681
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 12 weeks ago Marianna ▴ 20
3
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2
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497
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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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366
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Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
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2
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350
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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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386
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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
4
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4
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457
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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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602
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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
1
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8
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577
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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
0
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0
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267
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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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648
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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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380
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EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 3 months ago by 50k • written 4 months ago by • 0
3
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3
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716
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EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 4 months ago by 50k • written 4 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 Luca • 0
0
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1
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326
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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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642
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
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2
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493
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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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600
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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
1
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2
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458
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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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862
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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
50 results • Page 1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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