Showing : edgeR • reset
3
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2
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1.1k
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
15 months ago mohammedtoufiq91 ▴ 10
3
votes
3
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1.1k
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 15 months ago by 52k • written 15 months ago by • 0
1
vote
3
replies
982
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 15 months ago by 52k • written 15 months ago by • 0
0
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1
reply
588
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 16 months ago by 52k • written 16 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
16 months ago gene_bioconductor ▴ 10
1
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2
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1.5k
views
Citation for edgeR user guide
edgeR
written 16 months ago by ▴ 30
4
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6
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1.6k
views
FilterByExpr low counts with small sample size
edgeR
16 months ago Jonathan ▴ 10
0
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2
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620
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
16 months ago prity6459 • 0
0
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3
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882
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 16 months ago by 52k • written 16 months ago by • 0
5
votes
3
replies
1.5k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 16 months ago by 52k • written 16 months ago by • 0
3
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3
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1.7k
views
permutation test in edgeR
rna-seq edgeR
updated 16 months ago by 52k • written 17 months ago by • 0
1
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3
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877
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 16 months ago by 52k • written 17 months ago by • 0
5
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6
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1.3k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 16 months ago by ★ 4.9k • written 17 months ago by ▴ 70
1
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3
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787
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
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2
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843
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
17 months ago Marianna ▴ 20
0
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4
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1.3k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
17 months ago Lucy ▴ 60
3
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6
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2.1k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 17 months ago by • 0
0
votes
6
replies
1.2k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 17 months ago by 52k • written 17 months ago by • 0
0
votes
1
reply
987
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 17 months ago by 52k • written 17 months ago by • 0
8
votes
5
replies
3.0k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 10 months ago by 52k • written 17 months ago by ▴ 60
2
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3
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977
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 17 months ago by 52k • written 17 months ago by • 0
0
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2
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789
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 17 months ago by 52k • written 17 months ago by • 0
2
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2
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857
views
between lane normalization upper quantile
EDASeq edgeR
17 months ago elesofi • 0
2
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2
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739
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
17 months ago Sabiha ▴ 20
1
vote
3
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946
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 19 months ago by • 0
0
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1
reply
515
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 18 months ago by 52k • written 18 months ago by • 0
0
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11
replies
1.7k
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 18 months ago by 52k • written 18 months ago by • 0
0
votes
1
reply
665
views
ExactTest vs QLFTest
edgeR
updated 18 months ago by 52k • written 18 months ago by • 0
1
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7
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1.6k
views
Library size normalization in methylation count analysis
edgeR MethylationArray
updated 10 months ago by • 0 • written 18 months ago by • 0
2
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6
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952
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
18 months ago tsl0026 • 0
5
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4
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962
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
18 months ago pl23 • 0
0
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8
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1.6k
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
18 months ago Marianna ▴ 20
5
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2
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1.7k
views
How does one test for interactions in EdgeR?
edgeR
19 months ago • updated 18 months ago pl23 • 0
0
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4
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820
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Nested paired design
edgeR
19 months ago manduchi ▴ 10
1
vote
2
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1.0k
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
19 months ago mico • 0
2
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3
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982
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 19 months ago by 68k • written 19 months ago by • 0
4
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4
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875
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 19 months ago by 68k • written 19 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 19 months ago by 52k • written 19 months ago by • 0
1
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8
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1.4k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 19 months ago by 52k • written 19 months ago by • 0
0
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0
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889
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
19 months ago Jawahar • 0
2
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4
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2.0k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
19 months ago Sabiha ▴ 20
0
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3
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1.2k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 19 months ago by 52k • written 19 months ago by • 0
3
votes
3
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1.9k
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 19 months ago by 52k • written 19 months ago by • 0
4
votes
9
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2.3k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
20 months ago • updated 19 months ago Luca • 0
0
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1
reply
579
views
download problem
edgeR
updated 20 months ago by 52k • written 20 months ago by • 0
0
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5
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1.3k
views
Help with model for differential expression analysis
DifferentialExpression edgeR
20 months ago • updated 19 months ago Lucy ▴ 60
1
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2
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1.1k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
20 months ago Sabiha ▴ 20
5
votes
2
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1.4k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 21 months ago by 52k • written 21 months ago by • 0
1
vote
2
replies
1.3k
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 21 months ago by 52k • written 21 months ago by • 0
12
votes
5
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4.7k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 3 months ago by • 0 • written 21 months ago by • 0
2,027 results • Page 2 of 41
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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