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 7.5 years ago by ▴ 10
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
2
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3
replies
838
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
0
votes
9
replies
868
views
estimateDisp() error
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
1
vote
5
replies
695
views
edgeR design/contrast matrix troubles
edgeR
updated 8 months ago by 65k • written 8 months ago by • 0
2
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5
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1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
10 months ago • updated 9 months ago mohammedtoufiq91 ▴ 10
3
votes
4
replies
8.7k
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Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.9 years ago by ▴ 30
0
votes
4
replies
918
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 42k • written 9 months ago by • 0
1
vote
3
replies
368
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
1
vote
2
replies
456
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
4
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4
replies
456
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 4 months ago by • 0
0
votes
6
replies
370
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
9
votes
5
replies
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
6
votes
7
replies
968
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 7 months ago by ▴ 20
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 8 months ago by 50k • written 22 months ago by ▴ 30
0
votes
3
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479
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq edgeR
updated 26 days ago by 50k • written 5 weeks ago by • 0
1
vote
4
replies
761
views
MDS plot edgeR
edgeR
updated 7 months ago by 50k • written 8 months ago by ▴ 10
5
votes
9
replies
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 6.5 years ago by ▴ 10
0
votes
2
replies
305
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 29 days ago by • 0 • written 8.9 years ago by ▴ 30
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
1
vote
5
replies
882
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago duez.tolga • 0
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 11 months ago Luis • 0
1
vote
3
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439
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
0
votes
2
replies
499
views
EdgeR FTest
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
5
votes
2
replies
600
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
5
votes
3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 29 days ago by • 0
3
votes
3
replies
568
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
8 months ago Nisha • 0
1
vote
1
reply
409
views
A query about selecting the coefficient in glmLRT to test for by index
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
4
votes
12
replies
3.8k
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
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon edgeR
updated 6 months ago by 50k • written 3.6 years ago by ★ 4.1k
4
votes
6
replies
467
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 25 days ago Jonathan ▴ 10
1
vote
5
replies
756
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 8 months ago by 50k • written 8 months ago by ▴ 30
0
votes
1
reply
250
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
2
votes
4
replies
645
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
2
votes
6
replies
438
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago • updated 12 weeks ago tsl0026 • 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR edgeR
updated 6 weeks ago by 50k • written 12.5 years ago by ▴ 670
1
vote
2
replies
493
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.0 years ago by ▴ 60
2
votes
3
replies
386
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
5
votes
4
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428
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
2
votes
2
replies
2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 9 months ago by • 0 • written 6.4 years ago by • 0
0
votes
2
replies
147
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
28 days ago prity6459 • 0
0
votes
1
reply
511
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 8 months ago by ★ 4.1k • written 8 months ago by • 0
2
votes
1
reply
613
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
7
votes
2
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861
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
0
votes
11
replies
2.9k
views
edgeR contrasts
edgeR
updated 9 months ago by 65k • written 20 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
4
votes
2
replies
619
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
15 days ago • updated 11 days ago gene_bioconductor ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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