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4
votes
1
answer
71
views
1
answer
EdgeR blocking and "All combinations of multiple factors"
edger differential gene expression written 6 days ago by rfenouil • 0 • updated 6 days ago by James W. MacDonald ♦ 47k
8
votes
1
answer
60
views
1
answer
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect written 7 days ago by Laura • 20 • updated 7 days ago by Aaron Lun • 21k
2
votes
1
answer
81
views
1
answer
EdgeR analysis batch effect
edger differential gene expression written 7 days ago by rfenouil • 0 • updated 7 days ago by Aaron Lun • 21k
0
votes
1
answer
44
views
1
answer
Combining biological replicates from raw counts for use in differential gene expression/normalization (DESeq2 and edgeR)
differential gene expression biologicalreplicates raw_counts written 8 days ago by tasnif.rahman • 0 • updated 8 days ago by James W. MacDonald ♦ 47k
1
vote
1
answer
70
views
1
answer
How do I discern if a magnitude difference in expression is up-regulation in one group or down-regulation in another?
edger R differential gene expression gene list up-regulation written 12 days ago by philip.freda • 0 • updated 12 days ago by Gordon Smyth ♦ 35k
0
votes
0
answers
60
views
0
answers
Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
timecourse differential gene expression edge interaction written 5 weeks ago by rubi • 90
1
vote
2
answers
85
views
2
answers
skewed differentially expressed gene results - DESeq2
deseq2 differential gene expression outliers written 6 weeks ago by CE • 10 • updated 6 weeks ago by Ryan C. Thompson ♦ 6.8k
0
votes
0
answers
93
views
0
answers
Simple differential expression analysis for 2 groups
microarray limma differential gene expression agilent microarrays dea written 7 weeks ago by christiangriffioen • 0
1
vote
1
answer
88
views
1
answer
Differentially expressed genes across multiple conditions
differential gene expression limma voom multiple treatments written 9 weeks ago by vam3002 • 0 • updated 9 weeks ago by James W. MacDonald ♦ 47k
3
votes
1
answer
202
views
1
answer
EdgeR for differential analysis between two cell lines without replication
rnaseq edger differential gene expression written 10 weeks ago by Biologist • 70 • updated 10 weeks ago by Gordon Smyth ♦ 35k
0
votes
2
answers
83
views
2
answers
What are the different strategies to filter out low count genes?
rnaseq deseq2 differential gene expression written 10 weeks ago by ag1805x • 0 • updated 10 weeks ago by Wolfgang Huber ♦ 13k
5
votes
1
answer
186
views
1
answer
Possible ways to select differential expressed genes using DeSeq2 or edgeR
edger deseq2 R differential gene expression fold change written 10 weeks ago by Beginner • 50 • updated 10 weeks ago by Axel Klenk • 920
1
vote
1
answer
114
views
1
answer
Differential analysis based on selection of random samples
rnaseq deseq2 R bioconductor differential gene expression written 11 weeks ago by Beginner • 50 • updated 11 weeks ago by Michael Love ♦ 19k
1
vote
1
answer
68
views
1
answer
DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering written 11 weeks ago by mnaymik • 0 • updated 11 weeks ago by Michael Love ♦ 19k
1
vote
0
answers
100
views
0
answers
covariate vs adjustvars
rnaseq differential gene expression ballgown tuxedo written 11 weeks ago by justinjj • 10
1
vote
0
answers
104
views
0
answers
PROBLEM WHILE IMPORTING FOR edgeR
edger differential gene expression written 11 weeks ago by prakashpandey1111 • 0
2
votes
1
answer
87
views
1
answer
Differential analysis between 2 groups (n=1) vs (n=3) moderated t-test
limma differential gene expression moderated t-test small sample size written 11 weeks ago by mrupji • 0 • updated 11 weeks ago by Gordon Smyth ♦ 35k
1
vote
1
answer
101
views
1
answer
non-integer counts in DESeq2
deseq2 differential gene expression written 3 months ago by warrena • 0 • updated 3 months ago by Michael Love ♦ 19k
0
votes
1
answer
135
views
1
answer
Removing batch effect from gene expression before Limma linear modelling
limma differential gene expression covariates batch effect correction written 3 months ago by abelsousa • 0 • updated 3 months ago by Gordon Smyth ♦ 35k
0
votes
0
answers
89
views
0
answers
Ballgown normalisation... why are still using FPKM?
rnaseq normalization differential expression differential gene expression written 3 months ago by manuelmendoza • 0
6
votes
2
answers
201
views
2
answers
scaling data for clustering heat map
rnaseq clustering edger differential gene expression heatmap written 3 months ago by Beginner • 50 • updated 3 months ago by Gordon Smyth ♦ 35k
5
votes
2
answers
217
views
2
answers
Why DESeq2 and edgeR give different results?
rnaseq edger deseq2 differential gene expression written 3 months ago by Biologist • 70 • updated 3 months ago by Gordon Smyth ♦ 35k
4
votes
1
answer
155
views
1
answer
edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression design matrix model.matrix written 4 months ago by grabear • 0 • updated 4 months ago by Gordon Smyth ♦ 35k
4
votes
2
answers
276
views
2
answers
Filtering step for differential analysis in edgeR
edger R bioconductor differential gene expression filtering written 4 months ago by Biologist • 70 • updated 4 months ago by Gordon Smyth ♦ 35k
0
votes
1
answer
358
views
1
answer
TPM data Differential expression analysis
limma edger differential gene expression written 4 months ago by ghmdsr • 0 • updated 4 months ago by Gordon Smyth ♦ 35k
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