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7
votes
1
answer
180
views
1
answer
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq limma R logfc differential gene expression written 6 days ago by cms72 • 0 • updated 6 days ago by Aaron Lun • 15k
3
votes
2
answers
90
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2
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Does DEseq2 analysis make GOseq redundant?
goseq deseq2 gene ontology differential gene expression written 8 days ago by david.rinker • 0
0
votes
0
answers
51
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0
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design matrix and contrast for paired experiment using NanoStringDiff for nCounter data
design and contrast matrix differential gene expression nanostring nanostringdiff ncounter written 8 days ago by c.kohler • 0
4
votes
1
answer
73
views
1
answer
Multi-level experiment with limma
regression limma design and contrast matrix differential gene expression written 8 days ago by luca.piacentini • 0 • updated 8 days ago by Aaron Lun • 15k
4
votes
1
answer
156
views
1
answer
Question about decideTests function and adj.p.value in "limma" R Package
limma R differential gene expression written 9 days ago by ghk • 0 • updated 9 days ago by Gordon Smyth ♦ 30k
1
vote
1
answer
84
views
1
answer
Differential analysis with RSEM normalized counts using limma without voom
limma differential gene expression tcga rsem written 14 days ago by ghk • 0 • updated 14 days ago by James W. MacDonald ♦ 43k
1
vote
1
answer
623
views
1
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Low number differentially expressed genes with DESeq2, want to estimate dispersion gene-wise
rnaseq deseq2 differential gene expression written 2.3 years ago by A • 0
0
votes
0
answers
80
views
0
answers
cummeRbound problem when reading cuffdiff output
software error R differential gene expression written 21 days ago by ds920207 • 0
1
vote
1
answer
76
views
1
answer
Limma: model Design matrix and contrast matrix for getting gene log2 fold change data
bioconductor design and contrast matrix differential gene expression affymetrix microarrays written 26 days ago by raju.prasad.phe12 • 0 • updated 25 days ago by Aaron Lun • 15k
0
votes
0
answers
52
views
0
answers
Differential expressed genes between different samples in RUVseq
rnaseq R differential gene expression ruv written 4 weeks ago by manish20072013 • 0
0
votes
1
answer
99
views
1
answer
Why DESeq2 gives large logfold for group with all zero count?
microbiome deseq2 differential gene expression 16s written 6 weeks ago by lanhuong • 0
0
votes
1
answer
121
views
1
answer
Help with diff. expression analysis of Agilent files
microarray R agilent differential gene expression written 10 weeks ago by bhgyu • 0 • updated 10 weeks ago by Axel Klenk • 790
12
votes
1
answer
203
views
1
answer
Testing for DE genes
limma differential gene expression affymetrix microarrays written 10 weeks ago by Lennart.Vermander • 10 • updated 10 weeks ago by Aaron Lun • 15k
0
votes
1
answer
150
views
1
answer
how to extract complex contrast with DESeq2
deseq2 contrast differential gene expression written 11 weeks ago by aec • 30 • updated 11 weeks ago by Michael Love ♦ 13k
0
votes
1
answer
123
views
1
answer
Analysis small RNA data with DESeq2
deseq2 differential gene expression written 12 weeks ago by zcc_1127 • 0 • updated 11 weeks ago by Michael Love ♦ 13k
0
votes
1
answer
182
views
1
answer
DESeq2: use of unmix() function for deconvolution of whole blood
rnaseq deseq2 bioconductor differential gene expression written 12 weeks ago by nsimons • 0 • updated 12 weeks ago by Michael Love ♦ 13k
0
votes
1
answer
141
views
1
answer
Up and down regulation in LIMMA for microarray dataset
microarray limma differential gene expression written 3 months ago by danielle.newby • 0 • updated 3 months ago by Aaron Lun • 15k
0
votes
1
answer
189
views
1
answer
DESeq2 design formula/experiment table help
rnaseq deseq2 R differential gene expression written 3 months ago by greenhawmatt • 0 • updated 3 months ago by Michael Love ♦ 13k
0
votes
1
answer
195
views
1
answer
Calculate correlation matrix for gene expression data
R differential gene expression written 3 months ago by lvu2 • 0 • updated 3 months ago by sebastiano.curreli • 0
1
vote
1
answer
288
views
1
answer
Tutorial for RNA-Seq Data Analysis
rnaseq differential gene expression workflows tutorial data analysis written 3 months ago by Pranavathiyani G • 0 • updated 3 months ago by Aaron Lun • 15k
1
vote
1
answer
119
views
1
answer
DESeq2 high variance in differential expression results
deseq2 differential gene expression lrt variance written 3 months ago by rclaire • 0 • updated 3 months ago by Ryan C. Thompson ♦ 5.8k
0
votes
1
answer
134
views
1
answer
Different padj value after multiple testing
deseq2 differential gene expression padj multiple comparisons written 3 months ago by tarun2 • 0 • updated 3 months ago by Michael Love ♦ 13k
12
votes
1
answer
231
views
1
answer
How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
rnaseq edger differential gene expression written 4 months ago by gabriel.rosser • 20 • updated 4 months ago by Gordon Smyth ♦ 30k
0
votes
0
answers
125
views
0
answers
mulcom Error in input files
microarray error differential gene expression mulcom written 4 months ago by arronar • 0
3
votes
2
answers
226
views
2
answers
remove batch effect and adjusted model for 4 covariates in Limma
limma contrast differential gene expression batch effect covariates written 4 months ago by mheydarpour • 10
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