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0
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23
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0
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Error while loading the data structrure in the ballgown tool
rnaseq differential gene expression ballgown new tuxedo pipleine written 4 days ago by Mithil Gaikwad • 0
2
votes
1
answer
71
views
1
answer
Using LIMMA for differential gene analysis of microarray data
limma differential gene expression affymetrix microarrays ncbi geo written 9 days ago by Francesca McGrath • 0 • updated 9 days ago by Aaron Lun • 21k
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79
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1
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DESeq2 with several biological replicates
rnaseq deseq2 differential gene expression written 9 days ago by bharata1803 • 20
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1
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86
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1
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Apply different cutoffs with edgeR pipeline and glmTreat for RNA-Seq DEG analysis
edger differential gene expression glmtreat written 21 days ago by svlachavas • 610 • updated 15 days ago by Gordon Smyth ♦ 35k
2
votes
1
answer
85
views
1
answer
Multi-factor with interaction model in EdgeR and DESeq2
rnaseq edger deseq2 differential gene expression written 19 days ago by camilla.alves • 0 • updated 19 days ago by Michael Love ♦ 20k
9
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2
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129
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5 follow
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Finding DE genes from RNA-seq data
qvalue edger differential gene expression fpkm pvalue written 22 days ago by Harrisonesmith • 0 • updated 22 days ago by Steve Lianoglou ♦ 12k
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1
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69
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1
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Multiple factor design for differential expression with DESeq2
deseq2 differential gene expression multiple factor design written 26 days ago by galozs • 0 • updated 25 days ago by Michael Love ♦ 20k
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1
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72
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1
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DESEQ2 Finding Unchanged Genes
deseq2 differential gene expression written 4 weeks ago by tirza.doniger • 10 • updated 4 weeks ago by Michael Love ♦ 20k
5
votes
1
answer
114
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1
answer
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 design differential gene expression written 4 weeks ago by newbio17 • 0 • updated 4 weeks ago by Michael Love ♦ 20k
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1
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95
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1
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deseq2 analysis multiple factor and 4 different time points
differential gene expression bias edger and deseq2 written 5 weeks ago by yusuf.zhc • 0 • updated 5 weeks ago by swbarnes2 • 50
2
votes
1
answer
121
views
1
answer
How to block for a subject in a 2 factor design formula
rnaseq deseq2 differential gene expression written 5 weeks ago by Onyi Ukay • 0
1
vote
1
answer
91
views
1
answer
EdgeR between unequal group sizes?
rnaseq edger differential gene expression written 6 weeks ago by rina • 0 • updated 6 weeks ago by Gordon Smyth ♦ 35k
4
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1
answer
127
views
1
answer
EdgeR blocking and "All combinations of multiple factors"
edger differential gene expression written 9 weeks ago by rfenouil • 0 • updated 9 weeks ago by James W. MacDonald ♦ 48k
8
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1
answer
92
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1
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Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect written 9 weeks ago by Laura • 20 • updated 9 weeks ago by Aaron Lun • 21k
2
votes
1
answer
127
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1
answer
EdgeR analysis batch effect
edger differential gene expression written 9 weeks ago by rfenouil • 0 • updated 9 weeks ago by Aaron Lun • 21k
0
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1
answer
78
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 9 weeks ago by tasnif.rahman • 0 • updated 9 weeks ago by James W. MacDonald ♦ 48k
1
vote
1
answer
132
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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 10 weeks ago by philip.freda • 0 • updated 10 weeks ago by Gordon Smyth ♦ 35k
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86
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0
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Degrees of freedom and coefficients in an edge::deSet and edge::deFit objects
timecourse differential gene expression edge interaction written 3 months ago by rubi • 90
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2
answers
127
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2
answers
skewed differentially expressed gene results - DESeq2
deseq2 differential gene expression outliers written 3 months ago by CE • 10 • updated 3 months ago by Ryan C. Thompson ♦ 7.0k
0
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0
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120
views
0
answers
Simple differential expression analysis for 2 groups
microarray limma differential gene expression agilent microarrays dea written 3 months ago by christiangriffioen • 0
1
vote
1
answer
123
views
1
answer
Differentially expressed genes across multiple conditions
differential gene expression limma voom multiple treatments written 4 months ago by vam3002 • 0 • updated 4 months ago by James W. MacDonald ♦ 48k
3
votes
1
answer
261
views
1
answer
EdgeR for differential analysis between two cell lines without replication
rnaseq edger differential gene expression written 4 months ago by Biologist • 70 • updated 4 months ago by Gordon Smyth ♦ 35k
0
votes
2
answers
119
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2
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What are the different strategies to filter out low count genes?
rnaseq deseq2 differential gene expression written 4 months ago by ag1805x • 10 • updated 4 months ago by Wolfgang Huber ♦ 13k
5
votes
1
answer
251
views
1
answer
Possible ways to select differential expressed genes using DeSeq2 or edgeR
edger deseq2 R differential gene expression fold change written 4 months ago by Beginner • 50 • updated 4 months ago by Axel Klenk • 920
1
vote
1
answer
144
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1
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Differential analysis based on selection of random samples
rnaseq deseq2 R bioconductor differential gene expression written 4 months ago by Beginner • 50 • updated 4 months ago by Michael Love ♦ 20k
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