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6
votes
3
answers
118
views
3
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edgeR batch effect
bactch effect R design rna-seq edger written 4 days ago by NielQC • 10 • updated 2 days ago by Charles Warden ♦ 5.9k
2
votes
2
answers
770
views
5 follow
2
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Differential expression: replicates in one condition, no replicates in the other
rna-seq edger sequencing written 17 months ago by IP • 510 • updated 7 days ago by kristoffer.vittingseerup • 1.2k
17
votes
2
answers
372
views
10 follow
2
answers
How to see if adjusting batch effect in RNA-seq is working or not
removebatcheffect edger rna-seq batch effect written 11 days ago by iraia.munoa • 50 • updated 7 days ago by Charles Warden ♦ 5.9k
4
votes
1
answer
191
views
1
answer
RNAseq analysis: what comes first, filtering or normalization
R edger rna-seq written 19 days ago by Herbert • 0 • updated 19 days ago by h.mon ♦ 22k
3
votes
1
answer
190
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1
answer
Differential analysis with replicates using edgeR
differential analysis design matrix rna-seq edger written 6 weeks ago by Bioinfo • 270 • updated 26 days ago by Biostar ♦♦ 20
0
votes
1
answer
141
views
1
answer
A question about how the kegga function or KEGG analysis in general determines significance.
kegga rna-seq kegg edger limma written 4 weeks ago by brett.vanderwerff • 10
0
votes
0
answers
141
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0
answers
Different options tryed with DiffBind and did not know what final result believe
R diffbind deseq2 chip-seq edger written 4 weeks ago by iraia.munoa • 50
3
votes
1
answer
104
views
1
answer
EdgeR with Paired Sample Replicates
R edger rna-seq written 5 weeks ago by kmyers2 • 10 • updated 5 weeks ago by b.nota ♦ 5.7k
0
votes
0
answers
142
views
0
answers
DGE Analysis between 3 conditions
deseq rna-seq edger written 5 weeks ago by prabin.dm • 30
7
votes
3
answers
229
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5 follow
3
answers
Normalization for small non-coding RNA (piRNAs)
normalization deseq2 limma edger written 7 weeks ago by Konstantinos Yeles • 40 • updated 6 weeks ago by A. Domingues • 1.8k
8
votes
1
answer
194
views
1
answer
Too few differentially expressed genes identified by edgeR
edger written 8 weeks ago by afli • 150
0
votes
0
answers
170
views
0
answers
edgeR: how to make contrasts with makeContrasts
ngs makecontrasts glm edger dge written 9 weeks ago by m93 • 130
34
votes
3
answers
3.3k
views
16 follow
3
answers
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
gene limma edger written 14 months ago by Mike • 1.1k • updated 10 weeks ago by enxxx23 • 200
2
votes
2
answers
194
views
2
answers
Making a table of RNA seq results
R rna-seq edger written 10 weeks ago by tw617 • 20 • updated 10 weeks ago by zx8754 ♦ 6.2k
1
vote
1
answer
180
views
1
answer
How to make a gene expression correlation graph?
R rna-seq edger written 10 weeks ago by unawaz • 40 • updated 10 weeks ago by h.mon ♦ 22k
2
votes
1
answer
146
views
1
answer
How to identify differential expressed genes if the normalization assumptions are violated
deseq2 edger written 11 weeks ago by afli • 150 • updated 11 weeks ago by Devon Ryan ♦ 87k
2
votes
2
answers
133
views
2
answers
No replicates in 1 group, which idea is the best to apply?
no replicates deseq2 rna-seq edger written 12 weeks ago by Batu • 110 • updated 12 weeks ago by EagleEye ♦ 6.1k
0
votes
1
answer
346
views
1
answer
Should I remove samples after normalization of miRNA seq read counts ?
rna-seq edger mirnas written 11 months ago by Björn • 40 • updated 3 months ago by Biostar ♦♦ 20
1
vote
2
answers
249
views
2
answers
How to make cluster from gene read count?
R deseq2 rna-seq clustering edger written 3 months ago by ahmad mousavi • 350 • updated 3 months ago by Chirag Parsania • 1.3k
0
votes
0
answers
176
views
0
answers
DE Gene List to Regulatory Network
R de edger gene regulatory network written 3 months ago by gtasource • 20
4
votes
0
answers
281
views
0
answers
Is logCPM expression data good for plottinng?
plotting R geneexpression rna-seq edger written 3 months ago by Biologist • 110
3
votes
1
answer
340
views
1
answer
Advice on running a differential expression analysis on patients with slightly different mutations within each group
deseq2 rna-seq differential expression edger written 3 months ago by unawaz • 40
2
votes
1
answer
263
views
1
answer
design matrix for time point comparision [1 treatment] in time course RNA Seq - EdgeR
rna-seq edger masigpro written 4 months ago by thindmarsmission • 0 • updated 3 months ago by Antonio R. Franco • 3.9k
0
votes
1
answer
202
views
1
answer
How to create design matrix for confounder (here sunlight) in edgeR ?
rnaseq edger written 3 months ago by Björn • 40 • updated 3 months ago by b.nota ♦ 5.7k
7
votes
2
answers
394
views
8 follow
2
answers
Gene set enrichment analysis with edgeR output
R edger genesetenrichment gsea rna-seq written 3 months ago by Biologist • 110 • updated 3 months ago by h.mon ♦ 22k
1
vote
2
answers
1.2k
views
2
answers
TMM.normalized.FPKM vs .TMM.EXPR.matrix for populating SQL
trinity fpkm tpm sql edger written 2.3 years ago by ando.kelli • 40 • updated 3 months ago by egtabilin • 0
3
votes
0
answers
554
views
0
answers
Does FDR value change based Fold change cutoff?
R differential expression rna-seq edger statistics written 7 months ago by Biologist • 110 • updated 3 months ago by RamRS ♦ 20k
1
vote
1
answer
1.1k
views
1
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Error with combining samples into matrix using abundance_estimates_to_matrix.pl
matrix de edger rna-seq written 2.9 years ago by nikelle.petrillo • 90 • updated 3 months ago by RamRS ♦ 20k
1
vote
1
answer
165
views
1
answer
Fit GLM using part of the data
scrna-seq glm edger written 3 months ago by rasmus.agren • 0 • updated 3 months ago by Kevin Blighe ♦ 35k
0
votes
0
answers
257
views
0
answers
Problem with low count removal in edgeR ?
edger differential expression mirna written 4 months ago by Björn • 40
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