Showing : EdgeR • reset
2
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
7 days ago • updated 6 days ago mohammedtoufiq91 ▴ 10
2
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3
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183
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 13 days ago by 50k • written 13 days ago by • 0
1
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3
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294
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 14 days ago by 50k • written 15 days ago by • 0
0
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1
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189
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NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 26 days ago by 50k • written 26 days ago by • 0
4
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2
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661
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Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
26 days ago • updated 22 days ago gene_bioconductor ▴ 10
1
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2
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232
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Citation for edgeR user guide
edgeR
written 5 weeks ago by ▴ 30
4
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6
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501
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FilterByExpr low counts with small sample size
edgeR
5 weeks ago Jonathan ▴ 10
0
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2
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162
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
5 weeks ago prity6459 • 0
0
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3
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229
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
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3
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338
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Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 5 weeks ago by • 0
3
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3
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380
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permutation test in edgeR
rna-seq edgeR
updated 5 weeks ago by 50k • written 7 weeks ago by • 0
1
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3
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385
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
5
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6
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470
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 6 weeks ago by ★ 4.2k • written 7 weeks ago by ▴ 40
1
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3
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290
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 7 weeks ago by 66k • written 7 weeks ago by • 0
0
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2
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204
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
7 weeks ago Marianna ▴ 20
0
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4
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458
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
8 weeks ago Lucy ▴ 60
3
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5
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432
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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6
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389
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
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1
reply
265
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
5
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3
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769
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 9 weeks ago by ▴ 50
2
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3
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320
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
0
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2
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313
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
2
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2
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283
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between lane normalization upper quantile
EDASeq edgeR
10 weeks ago elesofi • 0
2
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2
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296
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 weeks ago Sabiha ▴ 20
1
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3
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454
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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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577
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 11 weeks ago by 50k • written 12 weeks ago by ▴ 50
0
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1
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247
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Different results from DGE using different subgroups in model.matrix
edgeR
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
0
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11
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818
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 12 weeks ago by 50k • written 3 months ago by • 0
0
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1
reply
308
views
ExactTest vs QLFTest
edgeR
updated 12 weeks ago by 50k • written 3 months ago by • 0
1
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6
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540
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Library size normalization in methylation count analysis
edgeR MethylationArray
3 months ago mico • 0
2
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6
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453
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edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago tsl0026 • 0
5
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4
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442
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Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago pl23 • 0
0
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8
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701
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago Marianna ▴ 20
3
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2
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524
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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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377
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Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
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2
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362
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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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404
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
4
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4
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471
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edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 4 months ago by 66k • written 4 months ago by • 0
6
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7
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627
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readDGE in edgeR giving me path names as sample names
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
1
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8
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601
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edgeR error "Design matrix not of full rank"
edgeR methylation
updated 4 months ago by 50k • written 4 months ago by • 0
0
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0
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282
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Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
4 months ago Jawahar • 0
2
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4
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679
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
0
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3
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418
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EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
3
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3
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748
views
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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1.2k
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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332
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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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656
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Help with model for differential expression analysis
DifferentialExpression edgeR
5 months ago • updated 4 months ago Lucy ▴ 60
1
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2
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511
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago Sabiha ▴ 20
5
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2
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623
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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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485
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 6 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Counter-directional LFC shrinkage by swbarnes2 ★ 1.4k
The y axes in those plots are logged. The average for condition1 is going to be higher than condition2 because of the very high outliers. …
Comment: Cannot install oligo on Fedora by Guido Hooiveld ★ 4.0k
Thanks for all suggestions and getting to the bottom of this! Unfortunately, fixing C code goes way above my skill level, so I cannot contr…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
I think the solution is for the C code in `oligo` to be updated to work with more modern versions of `zlib`. The `zlibbioc` package is real…
Comment: Error in gseDO function by Guido Hooiveld ★ 4.0k
I don't fully understand what you are asking... Yet, in my opinion it doesn't make sense to use the results of only 12 genes for ORA (nor G…
Comment: Counter-directional LFC shrinkage by ATpoint ★ 4.2k
Is this RNA-seq? The unshrunken MA-plot looks very odd and indicates that normalization is completely offset.
Votes
A: DESeq2: add annotations (from data frame) to DESeqDataSet
Answer: Error in gseDO function
Comment: what the test method for enrichGO in clusterProfiler?
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
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