Showing : edger • reset
1
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6
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2.7k
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Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.4 years ago by ▴ 10
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
2
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3
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797
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Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
9
votes
5
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5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
1
vote
5
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663
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edgeR design/contrast matrix troubles
edgeR
updated 7 months ago by 65k • written 7 months ago by • 0
0
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9
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837
views
estimateDisp() error
edgeR
updated 8 months ago by 50k • written 8 months ago by • 0
1
vote
2
replies
393
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
1
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4
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714
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MDS plot edgeR
edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 10
3
votes
4
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8.5k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 12 weeks ago by • 0 • written 10.8 years ago by ▴ 30
1
vote
3
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326
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 11 days ago by 50k • written 16 days ago by • 0
5
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9
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2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 8 months ago by • 0 • written 6.4 years ago by ▴ 10
0
votes
6
replies
316
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 27 days ago by 50k • written 28 days ago by • 0
6
votes
7
replies
921
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.0k • written 6 months ago by ▴ 20
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago mohammedtoufiq91 ▴ 10
4
votes
7
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13k
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Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 22 months ago by ▴ 30
0
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3
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442
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago • updated 4 months ago Karthik • 0
3
votes
3
replies
294
views
permutation test in edgeR
rna-seq edgeR
updated 5 days ago by 50k • written 18 days ago by • 0
4
votes
4
replies
421
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 12 weeks ago by 65k • written 3 months ago by • 0
5
votes
2
replies
536
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
2
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259
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
4
votes
9
replies
1.2k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 8 days ago by • 0 • written 8.8 years ago by ▴ 30
1
vote
5
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838
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
0
votes
4
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859
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 41k • written 8 months ago by • 0
1
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3
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383
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks ago by • 0
0
votes
2
replies
466
views
EdgeR FTest
edgeR
updated 8 months ago by 50k • written 8 months ago by • 0
2
votes
8
replies
2.2k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
12 months ago • updated 11 months ago Luis • 0
1
vote
2
replies
631
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 11 months ago by 50k • written 11 months ago by • 0
0
votes
3
replies
329
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EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
3
replies
537
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
7 months ago Nisha • 0
3
votes
1
reply
122
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 8 days ago by • 0
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 7 months ago by • 0 • written 3.2 years ago by • 0
1
vote
1
reply
395
views
A query about selecting the coefficient in glmLRT to test for by index
edgeR
updated 8 months ago by 50k • written 8 months ago by • 0
1
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5
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724
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 30
0
votes
11
replies
2.8k
views
edgeR contrasts
edgeR
updated 8 months ago by 65k • written 19 months ago by • 0
2
votes
1
reply
599
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 11 months ago by ★ 4.0k • written 11 months ago by • 0
4
votes
6
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338
views
FilterByExpr low counts with small sample size
edgeR
9 days ago • updated 4 days ago Jonathan ▴ 10
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon edgeR
updated 5 months ago by 50k • written 3.5 years ago by ★ 4.0k
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR edgeR
updated 27 days ago by 50k • written 12.4 years ago by ▴ 670
0
votes
1
reply
219
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
1
reply
625
views
Subtype specific differential expression analysis
R limmaGUI edgeR limma regutools
updated 12 months ago by 50k • written 12 months ago by • 0
2
votes
6
replies
396
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
10 weeks ago • updated 9 weeks ago tsl0026 • 0
2
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2
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2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 8 months ago by • 0 • written 6.4 years ago by • 0
0
votes
2
replies
91
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
7 days ago prity6459 • 0
2
votes
3
replies
355
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
0
votes
1
reply
493
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
3
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1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 3 months ago by 50k • written 3.0 years ago by ▴ 60
2
votes
4
replies
552
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
7
votes
2
replies
773
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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