Showing : EdgeR • reset
1
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 17 months ago by 53k • written 17 months ago by • 0
3
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5
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3.4k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 17 months ago by • 0 • written 21 months ago by ▴ 60
0
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4
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1.3k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
18 months ago vohara4 • 0
3
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6
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1.4k
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Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
18 months ago JG13 • 0
3
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2
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1.2k
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
18 months ago mohammedtoufiq91 ▴ 10
3
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3
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1.2k
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 19 months ago by 53k • written 19 months ago by • 0
1
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3
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1.1k
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 19 months ago by 53k • written 19 months ago by • 0
0
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1
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654
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 19 months ago by 53k • written 19 months ago by • 0
4
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2
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1.8k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
19 months ago gene_bioconductor ▴ 10
1
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2
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1.6k
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Citation for edgeR user guide
edgeR
written 19 months ago by ▴ 30
4
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6
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1.8k
views
FilterByExpr low counts with small sample size
edgeR
20 months ago • updated 19 months ago Jonathan ▴ 10
0
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2
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723
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
19 months ago prity6459 • 0
0
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3
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988
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 19 months ago by 53k • written 19 months ago by • 0
5
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3
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1.6k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 19 months ago by 53k • written 19 months ago by • 0
3
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3
replies
1.8k
views
permutation test in edgeR
rna-seq edgeR
updated 19 months ago by 53k • written 20 months ago by • 0
1
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3
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971
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 20 months ago by 53k • written 20 months ago by • 0
5
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6
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1.5k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 20 months ago by ★ 5.0k • written 20 months ago by ▴ 70
1
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3
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923
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by • 0
0
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2
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947
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
20 months ago Marianna ▴ 20
0
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4
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1.5k
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
20 months ago Lucy ▴ 60
3
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6
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2.3k
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Differing results from plotMDS and PCAtools
edgeR PCAtools
written 20 months ago by • 0
0
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6
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1.3k
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
0
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1
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1.1k
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Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
8
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5
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3.3k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 13 months ago by 53k • written 20 months ago by ▴ 60
2
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3
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1.1k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 21 months ago by 53k • written 21 months ago by • 0
0
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2
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884
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 21 months ago by 53k • written 21 months ago by • 0
2
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2
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959
views
between lane normalization upper quantile
EDASeq edgeR
21 months ago elesofi • 0
2
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2
replies
860
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
21 months ago Sabiha ▴ 20
1
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3
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1.0k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 22 months ago by • 0
0
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1
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565
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
0
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11
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1.9k
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 21 months ago by 53k • written 21 months ago by • 0
0
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1
reply
715
views
ExactTest vs QLFTest
edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
1
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7
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1.8k
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Library size normalization in methylation count analysis
edgeR MethylationArray
updated 13 months ago by • 0 • written 21 months ago by • 0
2
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6
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1.0k
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
22 months ago • updated 21 months ago tsl0026 • 0
5
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4
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1.1k
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Confusion about LFC using contrasts weights in EdgeR
edgeR
22 months ago • updated 21 months ago pl23 • 0
0
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8
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1.8k
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
22 months ago • updated 21 months ago Marianna ▴ 20
5
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2
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1.8k
views
How does one test for interactions in EdgeR?
edgeR
22 months ago pl23 • 0
0
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4
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925
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Nested paired design
edgeR
22 months ago manduchi ▴ 10
1
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2
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1.1k
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
22 months ago mico • 0
2
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3
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1.1k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 22 months ago by 68k • written 22 months ago by • 0
4
votes
4
replies
947
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 22 months ago by 68k • written 23 months ago by • 0
6
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7
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1.3k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
1
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8
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1.5k
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 22 months ago by 53k • written 22 months ago by • 0
0
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0
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944
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
22 months ago Jawahar • 0
2
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4
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2.2k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
22 months ago Sabiha ▴ 20
0
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3
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1.3k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 22 months ago by 53k • written 23 months ago by • 0
3
votes
3
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2.0k
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 23 months ago by 53k • written 23 months ago by • 0
4
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9
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2.4k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
23 months ago Luca • 0
0
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1
reply
625
views
download problem
edgeR
updated 23 months ago by 53k • written 23 months ago by • 0
0
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5
replies
1.4k
views
Help with model for differential expression analysis
DifferentialExpression edgeR
23 months ago • updated 22 months ago Lucy ▴ 60
2,031 results • Page 2 of 41
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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