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3
votes
1
answer
104
views
6 follow
1
answer
DE analysis with edgeR and possibly batch effect
de analysis edger batch effect written 3 days ago by seta • 1.1k • updated 3 days ago by Devon Ryan ♦ 88k
3
votes
1
answer
88
views
1
answer
Error in differential analysis for samples with different time points
differential analysis R rna-seq edger written 3 days ago by Biologist • 150 • updated 3 days ago by h.mon ♦ 24k
0
votes
1
answer
298
views
1
answer
How to extract normalized matrix after using calcNormFact function (with TMM method) ? edgeR
R edger rna-seq written 8 months ago by Katerina • 0 • updated 6 days ago by kristoffer.vittingseerup • 1.6k
0
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2
answers
126
views
2
answers
Query about gene ontology analysis in edgeR vs GSEA
edger go written 9 days ago by elizabethR • 70
0
votes
1
answer
101
views
1
answer
eclip-seq: Using edgeR/DESeq2 for normalizing peaks of IP/Input of transcript level
clip-seq eclip-seq deseq2 edger written 22 days ago by gnilihzeux • 0
2
votes
1
answer
93
views
1
answer
Using featureCounts Output for DE analysis in edgeR
featurecounts rna-seq edger written 20 days ago by markm014 • 0 • updated 20 days ago by Friederike ♦ 3.2k
0
votes
0
answers
87
views
0
answers
DE analysis of multiple time points and conditions
nested esign design matrix interaction edger written 4 weeks ago by scheitelt • 0
10
votes
1
answer
218
views
7 follow
1
answer
edgeR make contrast
contrasts rna-seq edger written 5 weeks ago by Bnf83 • 130 • updated 4 weeks ago by i.sudbery ♦ 4.0k
8
votes
1
answer
263
views
6 follow
1
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error while using edgeR( Negative counts not allowed)
R rna-seq edger written 5 weeks ago by deeksha3696 • 10 • updated 5 weeks ago by zx8754 ♦ 6.7k
2
votes
1
answer
161
views
1
answer
error while making a DEGList object on R using edgeR package
rna-seq edger written 5 weeks ago by saumya.sharma1509 • 0 • updated 5 weeks ago by WouterDeCoster ♦ 37k
6
votes
1
answer
126
views
1
answer
RNA-Seq: X samples and X batches
batch effects deseq2 rna-seq edger written 5 weeks ago by Behram Radmanesh • 10 • updated 5 weeks ago by WouterDeCoster ♦ 37k
9
votes
3
answers
939
views
6 follow
3
answers
Differential expression: replicates in one condition, no replicates in the other
rna-seq edger sequencing written 19 months ago by IP • 530 • updated 7 weeks ago by Gordon Smyth • 620
7
votes
3
answers
228
views
3
answers
edgeR batch effect
bactch effect R design rna-seq edger written 9 weeks ago by NielQC • 10 • updated 8 weeks ago by Charles Warden ♦ 6.4k
18
votes
2
answers
589
views
11 follow
2
answers
How to see if adjusting batch effect in RNA-seq is working or not
removebatcheffect edger rna-seq batch effect written 10 weeks ago by iraia.munoa • 60 • updated 9 weeks ago by Charles Warden ♦ 6.4k
4
votes
1
answer
293
views
1
answer
RNAseq analysis: what comes first, filtering or normalization
R edger rna-seq written 11 weeks ago by Herbert • 0 • updated 11 weeks ago by h.mon ♦ 24k
3
votes
1
answer
248
views
1
answer
Differential analysis with replicates using edgeR
differential analysis design matrix rna-seq edger written 3 months ago by Vasu • 320 • updated 12 weeks ago by Biostar ♦♦ 20
0
votes
1
answer
203
views
1
answer
A question about how the kegga function or KEGG analysis in general determines significance.
kegga rna-seq kegg edger limma written 3 months ago by brett.vanderwerff • 20
0
votes
0
answers
233
views
0
answers
Different options tryed with DiffBind and did not know what final result believe
R diffbind deseq2 chip-seq edger written 3 months ago by iraia.munoa • 60
3
votes
1
answer
158
views
1
answer
EdgeR with Paired Sample Replicates
R edger rna-seq written 3 months ago by kmyers2 • 20 • updated 3 months ago by b.nota ♦ 6.2k
0
votes
0
answers
207
views
0
answers
DGE Analysis between 3 conditions
deseq rna-seq edger written 3 months ago by prabin.dm • 30
7
votes
3
answers
310
views
5 follow
3
answers
Normalization for small non-coding RNA (piRNAs)
normalization deseq2 limma edger written 3 months ago by Konstantinos Yeles • 40 • updated 3 months ago by A. Domingues • 1.8k
8
votes
1
answer
287
views
1
answer
Too few differentially expressed genes identified by edgeR
edger written 4 months ago by afli • 170
0
votes
0
answers
324
views
0
answers
edgeR: how to make contrasts with makeContrasts
ngs makecontrasts glm edger dge written 4 months ago by m93 • 140
38
votes
3
answers
4.5k
views
18 follow
3
answers
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene limma edger written 16 months ago by Mike • 1.2k • updated 4 months ago by enxxx23 • 210
2
votes
2
answers
246
views
2
answers
Making a table of RNA seq results
R rna-seq edger written 4 months ago by tw617 • 20 • updated 4 months ago by zx8754 ♦ 6.7k
1
vote
1
answer
257
views
1
answer
How to make a gene expression correlation graph?
R rna-seq edger written 4 months ago by unawaz • 40 • updated 4 months ago by h.mon ♦ 24k
2
votes
1
answer
206
views
1
answer
How to identify differential expressed genes if the normalization assumptions are violated
deseq2 edger written 4 months ago by afli • 170 • updated 4 months ago by Devon Ryan ♦ 88k
2
votes
2
answers
174
views
2
answers
No replicates in 1 group, which idea is the best to apply?
no replicates deseq2 rna-seq edger written 4 months ago by Batu • 110 • updated 4 months ago by EagleEye ♦ 6.2k
0
votes
1
answer
396
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1
answer
Should I remove samples after normalization of miRNA seq read counts ?
rna-seq edger mirnas written 13 months ago by Björn • 40 • updated 5 months ago by Biostar ♦♦ 20
1
vote
2
answers
331
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2
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How to make cluster from gene read count?
R deseq2 rna-seq clustering edger written 5 months ago by ahmad mousavi • 410 • updated 5 months ago by Chirag Parsania • 1.4k
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