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Answer: Answer: Improving the design matrices vignette in RNAseq123
4 hours ago Gordon Smyth 50k
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83
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Answer: Answer: Citation for edgeR user guide
2 days ago Gordon Smyth 50k
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97
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Answer: Answer: limma-voom: Calculate the log-fold change in gene expression within a sample
3 days ago Gordon Smyth 50k
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781
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Answer: Answer: Why p value inconsistent when using different number of pathway score?
5 days ago Gordon Smyth 50k
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156
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Answer: Answer: RNAseq:Technical replicates from different batches
6 days ago Gordon Smyth 50k
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1
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336
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Answer: Answer: FilterByExpr low counts with small sample size
7 days ago Gordon Smyth 50k
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91
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Answer: Answer: How to make DGEList and design matrix by edgeR package
7 days ago Gordon Smyth 50k
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130
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Answer: Answer: Finding DEGs by using edgeR
7 days ago Gordon Smyth 50k
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121
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Answer: Answer: Log-cpm values from limma
7 days ago Gordon Smyth 50k
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254
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Answer: Answer: Methylation Analysis experiment design using Limma
9 days ago Gordon Smyth 50k
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162
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Answer: Answer: Differentially expressed genes in monocle pseudotime
10 days ago Gordon Smyth 50k
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292
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Answer: Answer: permutation test in edgeR
11 days ago • updated 5 days ago Gordon Smyth 50k
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326
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Answer: Answer: Why is my gene not significantly differentially expressed?
11 days ago Gordon Smyth 50k
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860
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Answer: Answer: Light difference when using coef vs omit a group when compare 3 groups.
14 days ago Gordon Smyth 50k
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147
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Answer: Answer: Limma design matrix only showing 3/4 treatments?
20 days ago Gordon Smyth 50k
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1
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415
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Answer: Answer: Using a change in a continuous explanatory variable to test changes in gene expr
22 days ago • updated 21 days ago Gordon Smyth 50k
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148
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Answer: Answer: edgeR analysis: glm functions and offset matrix
23 days ago Gordon Smyth 50k
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395
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Answer: Answer: Adjust RNA-seq counts (more than one batch variable) for plotting differentially
24 days ago Gordon Smyth 50k
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1.8k
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Answer: Answer: The difference when using Limma compare between 3 conditions vs 2 conditions
27 days ago • updated 20 days ago Gordon Smyth 50k
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316
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Answer: Answer: Doing comparison of RNA-seq data using EdgeR
28 days ago Gordon Smyth 50k
2
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340
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Answer: Answer: Differing results from plotMDS and PCAtools
28 days ago • updated 26 days ago Gordon Smyth 50k
1
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498
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Answer: Answer: Microarray Limma Model fitting and DEG
29 days ago Gordon Smyth 50k
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498
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Answer: Answer: Microarray Limma Model fitting and DEG
4 weeks ago Gordon Smyth 50k
2
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826
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Answer: Answer: limma models out of memory issue on Slurm HPC
4 weeks ago • updated 22 days ago Gordon Smyth 50k
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219
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Answer: Answer: Using splicing junction counts with edgeR/limma-voom
5 weeks ago Gordon Smyth 50k
2
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1
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688
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Answer: Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
5 weeks ago Gordon Smyth 50k
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280
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Answer: Answer: edgeR, 3 x 2 design with a batch effect and contrasts
5 weeks ago Gordon Smyth 50k
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430
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Answer: Answer: DEG Filtering
5 weeks ago Gordon Smyth 50k
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259
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Answer: Answer: RNAseq analysis
5 weeks ago Gordon Smyth 50k
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1
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245
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Answer: Answer: between lane normalization upper quantile
6 weeks ago Gordon Smyth 50k
2
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247
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Answer: Answer: Question about extracting co-efficients for pairwise comparisons in edgeR
6 weeks ago Gordon Smyth 50k
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411
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Answer: Answer: DESeq2 filtering vs edgeR filtering
6 weeks ago Gordon Smyth 50k
1
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0
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375
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Answer: Answer: Cross-species analysis - how to compute the mid parent value?
6 weeks ago Gordon Smyth 50k
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451
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Answer: Answer: limma: vooma mean-variance trend and data filtration
7 weeks ago Gordon Smyth 50k
2
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1
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482
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Answer: Answer: Constrast for Time Course Experiments using Limma
7 weeks ago Gordon Smyth 50k
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399
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Answer: Answer: Right way to pseudobulk donors across replicates in edgeR
7 weeks ago Gordon Smyth 50k
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212
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Answer: Answer: Different results from DGE using different subgroups in model.matrix
7 weeks ago Gordon Smyth 50k
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702
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Answer: Answer: Strange logFC values in differential methylation site anslysis
7 weeks ago Gordon Smyth 50k
2
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0
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428
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Answer: Answer: DGE analysis with LIMMA
7 weeks ago Gordon Smyth 50k
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0
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239
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Answer: Answer: ExactTest vs QLFTest
8 weeks ago • updated 7 weeks ago Gordon Smyth 50k
0
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1
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272
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Answer: Answer: Differential enrichment analysis
8 weeks ago Gordon Smyth 50k
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0
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269
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Answer: Answer: Error in featureCounts matrix
8 weeks ago Gordon Smyth 50k
0
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1
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456
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Answer: Answer: Library size normalization in methylation count analysis
8 weeks ago Gordon Smyth 50k
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1
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535
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Answer: Answer: limma fo continous variables
9 weeks ago Gordon Smyth 50k
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1
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274
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Answer: Answer: limma model matrix questions
9 weeks ago Gordon Smyth 50k
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306
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Answer: Answer: Limma with replicates at different time points
9 weeks ago Gordon Smyth 50k
0
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0
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212
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Answer: Answer: Main effect on multiple comparisons in limma
9 weeks ago Gordon Smyth 50k
1
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1
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396
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Answer: Answer: edgeR: DEGs in a CRD factorial (2x2x2)
9 weeks ago Gordon Smyth 50k
2
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1
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380
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Answer: Answer: Confusion about LFC using contrasts weights in EdgeR
9 weeks ago Gordon Smyth 50k
2
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0
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282
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Answer: Answer: Normalization factors when there is a possible unidirectional expression
10 weeks ago Gordon Smyth 50k
2,670 results • Page 1 of 54
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