Showing : edgeR • reset
2
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2
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118
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
3 days ago • updated 2 days ago mohammedtoufiq91 ▴ 10
2
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3
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175
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How to correctly adjust for gender in edgeR
design glm edgeR
updated 8 days ago by 50k • written 9 days ago by • 0
1
vote
3
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286
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 9 days ago by 50k • written 10 days ago by • 0
0
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1
reply
184
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 21 days ago by 50k • written 22 days ago by • 0
4
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2
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651
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
22 days ago • updated 18 days ago gene_bioconductor ▴ 10
1
vote
2
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222
views
Citation for edgeR user guide
edgeR
written 4 weeks ago by ▴ 30
4
votes
6
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493
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FilterByExpr low counts with small sample size
edgeR
5 weeks ago • updated 4 weeks ago Jonathan ▴ 10
0
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2
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159
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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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225
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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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331
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Log-cpm values from limma
limma edgeR RNASeq
updated 14 days ago by 50k • written 5 weeks ago by • 0
3
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3
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374
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permutation test in edgeR
rna-seq edgeR
updated 4 weeks ago by 50k • written 6 weeks ago by • 0
1
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3
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375
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
5
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6
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468
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.2k • written 6 weeks ago by ▴ 40
1
vote
3
replies
286
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 6 weeks ago by 66k • written 7 weeks ago by • 0
0
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2
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201
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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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450
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
7 weeks ago Lucy ▴ 60
3
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5
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423
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Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
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6
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380
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
1
reply
261
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
votes
3
replies
759
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
votes
3
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318
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
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2
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308
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 weeks ago by 50k • written 10 weeks ago by • 0
2
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2
replies
281
views
between lane normalization upper quantile
EDASeq edgeR
10 weeks ago • updated 9 weeks ago elesofi • 0
2
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2
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294
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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
vote
3
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448
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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554
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 11 weeks ago by 50k • written 11 weeks ago by ▴ 50
0
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1
reply
244
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
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11
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813
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
0
votes
1
reply
300
views
ExactTest vs QLFTest
edgeR
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
1
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6
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539
views
Library size normalization in methylation count analysis
edgeR MethylationArray
12 weeks ago mico • 0
2
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6
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450
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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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441
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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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693
views
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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518
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
0
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4
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374
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
vote
2
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357
views
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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399
views
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
replies
468
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 66k • written 4 months ago by • 0
6
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7
replies
622
views
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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597
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 4 months ago by • 0
0
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0
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275
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
4 months ago Jawahar • 0
2
votes
4
replies
668
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
0
votes
3
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402
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
3
replies
744
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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1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago Luca • 0
0
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1
reply
328
views
download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
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5
replies
653
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
vote
2
replies
503
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago Sabiha ▴ 20
5
votes
2
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614
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
1
vote
2
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475
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
50 results • Page 1 of 1
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Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function by Robert Castelo ★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Comment: Cannot install oligo on Fedora by Guido Hooiveld ★ 4.0k
Aha, that is a good one! Starting from release 40, as I just found out, Fedora apparently is not including/using `zlib` as such anymore, b…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
What version of zlib are you running? I can compile with 1.2.7
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Seurat/DESeq2 - single cell RNA-seq differential expression
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