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1
vote
2
answers
134
views
2
answers
Comparison between limma and edgeR of reads ratio
limma edger offset written 4 days ago by catpaw.tw • 0 • updated 1 day ago by Gordon Smyth ♦ 33k
2
votes
1
answer
64
views
1
answer
EdgeR: Prior degrees of freedom effect on tag wise dispersion
rnaseq edger R rna-seq written 2 days ago by r.beeloo • 0 • updated 2 days ago by Aaron Lun • 19k
1
vote
1
answer
63
views
1
answer
how to create csv file with name of gene from unique ID of lcpm ?
edger bioconductor lcpm written 6 days ago by Björn • 0 • updated 6 days ago by Michael Love ♦ 17k
4
votes
1
answer
68
views
1
answer
edgeR error when trying to filter peaks with low read counts
edger R filtering written 6 days ago by camerond • 0
1
vote
2
answers
42
views
2
answers
edgeR/DGEList add assays to a DGEList like in SummarizedExperiment
edger dgelist summarizedexperiment written 6 days ago by aljoscha.leusmann • 0
4
votes
1
answer
58
views
1
answer
edgeR: Choice of reference group in nested model
edger reference group nested design model.matrix written 7 days ago by ri.lars • 40 • updated 7 days ago by Aaron Lun • 19k
8
votes
2
answers
78
views
2
answers
read counts for gene families
edger written 9 days ago by zhou_hye • 10 • updated 9 days ago by Gordon Smyth ♦ 33k
4
votes
2
answers
73
views
2
answers
Separate listing of up-regulated and down-regulated genes in edgeR DGE results.
edger differential gene expression upregulated genes downregulated genes written 13 days ago by fawazfebin • 30 • updated 11 days ago by lisacarlon25 • 0
5
votes
1
answer
54
views
1
answer
edgeR normalisation factors different between experimental groups
edger written 12 days ago by maltethodberg • 50 • updated 12 days ago by Aaron Lun • 19k
1
vote
1
answer
75
views
1
answer
Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions differential gene expression multiple factor design written 15 days ago by David Rengel • 70
2
votes
1
answer
49
views
1
answer
Repeated Measures, Within-Subject, Between-Groups RNAseq Analysis
rnaseq edger repeated measures written 15 days ago by wjh180 • 0 • updated 15 days ago by Ryan C. Thompson ♦ 6.5k
0
votes
1
answer
377
views
1
answer
Differential expression testing for groups with unequal variances/dispersions?
edger written 4.9 years ago by Ryan C. Thompson ♦ 6.5k • updated 15 days ago by sgupt46 • 0
4
votes
1
answer
76
views
1
answer
How does edgeR cpm function calculate log(CPM) values?
edger cpm written 18 days ago by jxb.dev • 0 • updated 18 days ago by James W. MacDonald ♦ 46k
0
votes
1
answer
50
views
1
answer
error: NA counts not permitted
edger systempiper rna-seq written 19 days ago by clarisbaby • 0 • updated 19 days ago by Aaron Lun • 19k
3
votes
2
answers
90
views
2
answers
EdgeR model formula design matrix
edger design matrix paired samples written 20 days ago by aiko • 0 • updated 20 days ago by Aaron Lun • 19k
4
votes
1
answer
69
views
1
answer
How does the function model.matrix (to define experimental design) really works ?
edger experimental design model.matrix written 28 days ago by Aurora • 10 • updated 28 days ago by Ryan C. Thompson ♦ 6.5k
0
votes
1
answer
64
views
1
answer
filtering lowly expressed genes before or after normalization?
edger tximport written 5 weeks ago by burcu.atasu • 0 • updated 5 weeks ago by Michael Love ♦ 17k
0
votes
1
answer
80
views
1
answer
differential expression analysis of cell subtypes mixture
edger deseq2 design matrix multifactorial design written 5 weeks ago by Assa Yeroslaviz • 1.4k • updated 5 weeks ago by Aaron Lun • 19k
6
votes
1
answer
119
views
1
answer
Fitting Gamma GLMs for examining differential expression
edger deseq2 differential expression written 5 weeks ago by jspmccain • 10 • updated 5 weeks ago by Ryan C. Thompson ♦ 6.5k
0
votes
0
answers
55
views
0
answers
Using edgeR to analyze Cripsr/Cas9 Screening data
edger processamplicons sgrna crispr written 5 weeks ago by Assa Yeroslaviz • 1.4k
0
votes
0
answers
34
views
0
answers
using the edgeR for sgRNA workflow with my own data
edger processamplicons sgrna written 5 weeks ago by Assa Yeroslaviz • 1.4k
0
votes
1
answer
101
views
1
answer
edgeR design matrix
edger design and contrast matrix design matrix written 5 weeks ago by cafelumiere12 • 20 • updated 5 weeks ago by Gordon Smyth ♦ 33k
3
votes
1
answer
117
views
1
answer
Difficulties with probable batch effect in paired blocked (treatment and placebo) experiment
limma edger deseq2 batch effect paired design written 5 weeks ago by Vladimir Krasikov • 90
0
votes
0
answers
52
views
0
answers
How to find back the list of genes involved in pathways produced by a kegg analysis (kegga) with limma package
edger kegg written 5 weeks ago by jambroise83 • 0
1
vote
1
answer
82
views
1
answer
EdgeR model matrix: interaction term
edger written 6 weeks ago by fcamus • 0 • updated 6 weeks ago by Aaron Lun • 19k
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