Showing : EDGER • reset
1
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 15 months ago by 53k • written 16 months ago by • 0
3
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5
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3.2k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 16 months ago by • 0 • written 20 months ago by ▴ 60
0
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4
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1.1k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
16 months ago vohara4 • 0
3
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6
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1.3k
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Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
17 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
17 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 17 months ago by 53k • written 17 months ago by • 0
1
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3
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1.1k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 17 months ago by 53k • written 17 months ago by • 0
0
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1
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623
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 18 months ago by 53k • written 18 months ago by • 0
4
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2
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1.7k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
18 months ago gene_bioconductor ▴ 10
1
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2
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1.5k
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Citation for edgeR user guide
edgeR
written 18 months ago by ▴ 30
4
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6
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1.7k
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FilterByExpr low counts with small sample size
edgeR
18 months ago Jonathan ▴ 10
0
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2
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672
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
18 months ago prity6459 • 0
0
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3
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943
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 18 months ago by 53k • written 18 months ago by • 0
5
votes
3
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1.5k
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Log-cpm values from limma
limma edgeR RNASeq
updated 17 months ago by 53k • written 18 months ago by • 0
3
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3
replies
1.8k
views
permutation test in edgeR
rna-seq edgeR
updated 18 months ago by 53k • written 19 months ago by • 0
1
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3
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933
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 18 months ago by 53k • written 18 months ago by • 0
5
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6
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1.4k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by ▴ 70
1
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3
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873
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
0
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2
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902
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
19 months ago Marianna ▴ 20
0
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4
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1.4k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
19 months ago Lucy ▴ 60
3
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6
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2.2k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 19 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 19 months ago by 53k • written 19 months ago by • 0
0
votes
1
reply
1.0k
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 19 months ago by 53k • written 19 months ago by • 0
8
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5
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3.2k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 12 months ago by 53k • written 19 months ago by ▴ 60
2
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3
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1.0k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 19 months ago by 53k • written 19 months ago by • 0
0
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2
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843
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 19 months ago by 53k • written 19 months ago by • 0
2
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2
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910
views
between lane normalization upper quantile
EDASeq edgeR
19 months ago elesofi • 0
2
votes
2
replies
811
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
19 months ago Sabiha ▴ 20
1
vote
3
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994
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 21 months ago by • 0
0
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1
reply
544
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
0
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11
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1.8k
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 20 months ago by 53k • written 20 months ago by • 0
0
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1
reply
698
views
ExactTest vs QLFTest
edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
1
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7
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1.7k
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Library size normalization in methylation count analysis
edgeR MethylationArray
updated 12 months ago by • 0 • written 20 months ago by • 0
2
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6
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1.0k
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
20 months ago tsl0026 • 0
5
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4
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1.0k
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Confusion about LFC using contrasts weights in EdgeR
edgeR
20 months ago pl23 • 0
0
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8
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1.7k
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
20 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
20 months ago pl23 • 0
0
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4
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873
views
Nested paired design
edgeR
21 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
21 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 21 months ago by 68k • written 21 months ago by • 0
4
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4
replies
924
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 21 months ago by 68k • written 21 months ago by • 0
6
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7
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1.2k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
1
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8
replies
1.5k
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 21 months ago by 53k • written 21 months ago by • 0
0
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0
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921
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
21 months ago Jawahar • 0
2
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4
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2.1k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
21 months ago Sabiha ▴ 20
0
votes
3
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1.3k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
3
votes
3
replies
1.9k
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
4
votes
9
replies
2.4k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
22 months ago • updated 21 months ago Luca • 0
0
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1
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611
views
download problem
edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
0
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5
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1.4k
views
Help with model for differential expression analysis
DifferentialExpression edgeR
22 months ago • updated 21 months ago Lucy ▴ 60
2,031 results • Page 2 of 41
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
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Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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