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Comment: Comment: Pipeline for an Anova-like analysis in edgeR
13 hours ago Gordon Smyth 42k
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90
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Answer: Answer: Pipeline for an Anova-like analysis in edgeR
1 day ago Gordon Smyth 42k
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147
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Answer: Answer: How to apply limma-trend or voom to batch corrected single cell data? (non-integ
4 days ago • updated 2 days ago Gordon Smyth 42k
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124
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Answer: Answer: Sample quality weights for RNA-seq
6 days ago Gordon Smyth 42k
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107
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Comment: Comment: Fitting a continuous variable with batch effect using Limma. Also a question abo
9 days ago Gordon Smyth 42k
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107
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Answer: Answer: Fitting a continuous variable with batch effect using Limma. Also a question abo
9 days ago Gordon Smyth 42k
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122
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Comment: Comment: edgeR for a mixture experiment
10 days ago Gordon Smyth 42k
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122
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Answer: Answer: edgeR for a mixture experiment
10 days ago Gordon Smyth 42k
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Answer: Answer: NChannelSet --> eSet/expressionSet ? How to transform?
10 days ago Gordon Smyth 42k
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279
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Job: Bioinformatics Laboratory Head, WEHI, Melbourne, Australia
JobPosting Australia
11 days ago • updated 22 hours ago Gordon Smyth 42k
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121
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Answer: Answer: Differential Transcript Usage: complex factorial design
12 days ago Gordon Smyth 42k
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66
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Answer: Answer: While I'm using edgeR how can I convert a .txt file and .tabular file into .RDat
15 days ago Gordon Smyth 42k
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92
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Answer: Answer: How do I set up a contrast matrix in edgeR with makeContrasts, when a relevant l
15 days ago Gordon Smyth 42k
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79
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Answer: Answer: I want to use global test.
15 days ago Gordon Smyth 42k
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148
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Comment: Comment: While trying to remove non differentially expressed genes through limma, I am ge
16 days ago Gordon Smyth 42k
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148
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Comment: Comment: While trying to remove non differentially expressed genes through limma, I am ge
16 days ago Gordon Smyth 42k
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148
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Answer: Answer: While trying to remove non differentially expressed genes through limma, I am ge
16 days ago • updated 15 days ago Gordon Smyth 42k
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156
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Answer: Answer: multifactorial design matrix
18 days ago Gordon Smyth 42k
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830
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Comment: Comment: RPKM normalization for several samples using a for loop
19 days ago Gordon Smyth 42k
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137
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Answer: Answer: GEO + RNA-seq. Total Newbie.
19 days ago Gordon Smyth 42k
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93
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Answer: Answer: Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
20 days ago Gordon Smyth 42k
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99
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Answer: Answer: voom-limma workflow for RNAseq samples with very different numbers of counts
23 days ago Gordon Smyth 42k
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105
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Answer: Answer: Alternative splicing analysis in edgeR: duplicate exons
26 days ago • updated 24 days ago Gordon Smyth 42k
2
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123
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Answer: Answer: Multi-level comparisons with paired data: duplicateCorrelation or not?
27 days ago Gordon Smyth 42k
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0
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99
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Answer: Answer: Remove genes before normalization?
27 days ago Gordon Smyth 42k
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96
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Answer: Answer: Get the latest gene name from Entrez ID
28 days ago Gordon Smyth 42k
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98
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Answer: Answer: Technical-biological replicates in edgeR
29 days ago Gordon Smyth 42k
2
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134
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Comment: Comment: Differential protein/biomarker expression using limma: is that possible?
4 weeks ago Gordon Smyth 42k
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187
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Comment: Comment: Discrepancy in effect size calculation between ordinary Cohens D and LIMMA
4 weeks ago Gordon Smyth 42k
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0
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105
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Comment: Comment: Bioconductor packages for doing tRNA seq analysis
5 weeks ago Gordon Smyth 42k
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105
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Comment: Comment: Bioconductor packages for doing tRNA seq analysis
5 weeks ago Gordon Smyth 42k
0
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555
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Comment: Comment: What is the correct use of removeBatchEffect's design parameter
5 weeks ago • updated 4 weeks ago Gordon Smyth 42k
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555
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Comment: Comment: What is the correct use of removeBatchEffect's design parameter
5 weeks ago Gordon Smyth 42k
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96
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Answer: Answer: time couse RNAseq experiment 2 treatments x 4 times
5 weeks ago Gordon Smyth 42k
2
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187
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Answer: Answer: Discrepancy in effect size calculation between ordinary Cohens D and LIMMA
5 weeks ago Gordon Smyth 42k
2
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0
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240
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Comment: Comment: limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PRO
5 weeks ago Gordon Smyth 42k
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134
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Answer: Answer: Differential protein/biomarker expression using limma: is that possible?
5 weeks ago Gordon Smyth 42k
1
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0
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78
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Answer: Answer: Error occured in designing a matrix
5 weeks ago Gordon Smyth 42k
1
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1
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240
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Comment: Comment: limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PRO
5 weeks ago Gordon Smyth 42k
1
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1
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240
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Comment: Comment: limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PRO
5 weeks ago Gordon Smyth 42k
0
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0
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83
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Answer: Answer: Is there is any distribution assumption for voom tranformed matrix?
5 weeks ago Gordon Smyth 42k
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240
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Answer: Answer: [limma:arrayWeights() ] for biological replicates? (PROTEOMICS)
5 weeks ago Gordon Smyth 42k
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121
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Answer: Answer: edgeR - Chapter 4.8 Time Course RNAseq experiments
5 weeks ago Gordon Smyth 42k
3
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144
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Answer: Answer: Weird MAplot with DEGs lying along the diagonals
5 weeks ago Gordon Smyth 42k
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1
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320
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Comment: Comment: Using edgeR and a spike-in to calculate absolute abundance
6 weeks ago Gordon Smyth 42k
0
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120
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Comment: Comment: add group info within DGE-object before TMM normalization
6 weeks ago Gordon Smyth 42k
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114
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Comment: Comment: How to calculate coefficient of variation within group?
6 weeks ago • updated 5 weeks ago Gordon Smyth 42k
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120
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Answer: Answer: add group info within DGE-object before TMM normalization
6 weeks ago Gordon Smyth 42k
0
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1
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114
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Answer: Answer: How to calculate coefficient of variation within group?
6 weeks ago Gordon Smyth 42k
1
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1
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320
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Comment: Comment: Using edgeR and a spike-in to calculate absolute abundance
6 weeks ago Gordon Smyth 42k
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