Showing : edger • reset
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 23 months ago by ▴ 30
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 4 months ago by • 0 • written 7.2 years ago by • 0
3
votes
4
replies
8.7k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.9 years ago by ▴ 30
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 4 weeks ago by • 0 • written 8.9 years ago by ▴ 30
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
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
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 12 months ago by ▴ 20
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
0
votes
11
replies
2.9k
views
edgeR contrasts
edgeR
updated 9 months ago by 66k • written 20 months ago by • 0
1
vote
6
replies
2.7k
views
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
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 9 months ago by • 0 • written 6.5 years ago by ▴ 10
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
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
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
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 7 weeks ago by 50k • written 11.5 years ago by ▴ 30
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 3.1 years ago by ▴ 60
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 4 weeks ago by • 0 • written 15 months ago by ▴ 10
0
votes
1
reply
1.5k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 5 months ago by 50k • written 10.3 years ago by ★ 13k
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
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
10 months ago mohammedtoufiq91 ▴ 10
0
votes
8
replies
1.4k
views
Question about filterByExpr function edgeR
edgeR
9 months ago lucap • 0
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
10 months ago Luca • 0
0
votes
3
replies
1.3k
views
EdgeR glm based analysis
edgeR edgeR
10.4 years ago • updated 9 months ago Gordon Smyth 50k
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 12 months ago by 50k • written 12 months ago by ▴ 10
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago Luca • 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR edgeR
updated 7 weeks ago by 50k • written 12.5 years ago by ▴ 670
4
votes
3
replies
1.1k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
0
replies
994
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
8 months ago Gordon Smyth 50k
6
votes
7
replies
979
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 7 months ago by ★ 4.1k • written 7 months ago by ▴ 20
0
votes
4
replies
930
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
5
replies
889
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago duez.tolga • 0
0
votes
9
replies
875
views
estimateDisp() error
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
7
votes
2
replies
869
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
3
votes
6
replies
863
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
2
votes
3
replies
846
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
1
vote
2
replies
842
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
8 months ago petertam1343 • 0
0
votes
5
replies
826
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 11 months ago by 66k • written 11 months ago by • 0
0
votes
11
replies
800
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
1
vote
4
replies
762
views
MDS plot edgeR
edgeR
updated 8 months ago by 50k • written 8 months ago by ▴ 10
1
vote
5
replies
761
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
6
votes
2
replies
748
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
10 months ago Josué ▴ 20
5
votes
3
replies
745
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
3
votes
3
replies
730
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
0
votes
2
replies
713
views
EdgeR and repeated measures: how to design a correct matrix having three time points
repeatedmeasure edgeR
9 months ago greta • 0
1
vote
5
replies
700
views
edgeR design/contrast matrix troubles
edgeR
updated 8 months ago by 66k • written 8 months ago by • 0
0
votes
8
replies
691
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago Marianna ▴ 20
3
votes
2
replies
690
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 11 months ago by 50k • written 11 months ago by ▴ 10
4
votes
2
replies
685
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
2
votes
4
replies
654
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
0
votes
5
replies
647
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
50 results • Page 1 of 1
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Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
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Hello everyone, I am new on this site but not a noob in R (I guess). I am facing the same problem. For me, it depends on the NOIseq plot fu…
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Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
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Yes, you can use `limma`.
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You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
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how to control age and gender effect in expression data using DESeq2
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