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Comment:
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
20 hours ago
Gordon Smyth
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263
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Answer:
Answer: Microarray Limma Model fitting and DEG
21 hours ago • updated 14 hours ago
Gordon Smyth
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0
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321
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Comment:
Comment: DEG Filtering
22 hours ago
Gordon Smyth
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263
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Answer:
Answer: Microarray Limma Model fitting and DEG
1 day ago
Gordon Smyth
50k
0
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0
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118
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Comment:
Comment: limma models out of memory issue on Slurm HPC
2 days ago
Gordon Smyth
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1
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118
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Answer:
Answer: limma models out of memory issue on Slurm HPC
2 days ago
Gordon Smyth
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2
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323
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Comment:
Comment: Batch Effect Correction, Gene Filtering
5 days ago
Gordon Smyth
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1
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323
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Comment:
Comment: Batch Effect Correction, Gene Filtering
5 days ago
Gordon Smyth
50k
0
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0
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144
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Answer:
Answer: Using splicing junction counts with edgeR/limma-voom
6 days ago
Gordon Smyth
50k
2
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1
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382
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Answer:
Answer: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
7 days ago
Gordon Smyth
50k
1
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1
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321
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Comment:
Comment: DEG Filtering
8 days ago • updated 5 days ago
Gordon Smyth
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1
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1
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321
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Comment:
Comment: DEG Filtering
9 days ago
Gordon Smyth
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1
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0
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217
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Comment:
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
9 days ago
Gordon Smyth
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217
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Answer:
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
9 days ago
Gordon Smyth
50k
0
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1
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323
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Comment:
Comment: limma: vooma mean-variance trend and data filtration
10 days ago
Gordon Smyth
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126
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Comment:
Comment: Rsubread: buildindex() should support multiple reference files
11 days ago
Gordon Smyth
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2
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1
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321
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Answer:
Answer: DEG Filtering
11 days ago • updated 10 days ago
Gordon Smyth
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0
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0
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211
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Answer:
Answer: RNAseq analysis
12 days ago
Gordon Smyth
50k
1
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1
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197
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Answer:
Answer: between lane normalization upper quantile
13 days ago
Gordon Smyth
50k
2
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1
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187
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Answer:
Answer: Question about extracting co-efficients for pairwise comparisons in edgeR
14 days ago
Gordon Smyth
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0
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1
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338
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Answer:
Answer: DESeq2 filtering vs edgeR filtering
14 days ago
Gordon Smyth
50k
0
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1
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323
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Comment:
Comment: limma: vooma mean-variance trend and data filtration
16 days ago
Gordon Smyth
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0
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0
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306
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Answer:
Answer: Cross-species analysis - how to compute the mid parent value?
19 days ago
Gordon Smyth
50k
0
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1
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323
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Answer:
Answer: limma: vooma mean-variance trend and data filtration
21 days ago • updated 20 days ago
Gordon Smyth
50k
0
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1
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415
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Comment:
Comment: Constrast for Time Course Experiments using Limma
21 days ago
Gordon Smyth
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2
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1
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415
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Answer:
Answer: Constrast for Time Course Experiments using Limma
21 days ago
Gordon Smyth
50k
0
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0
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211
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Comment:
Comment: Differential enrichment analysis
22 days ago
Gordon Smyth
50k
1
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0
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287
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Answer:
Answer: Right way to pseudobulk donors across replicates in edgeR
22 days ago
Gordon Smyth
50k
1
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1
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415
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Comment:
Comment: Constrast for Time Course Experiments using Limma
22 days ago
Gordon Smyth
50k
0
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0
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586
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Comment:
Comment: Strange logFC values in differential methylation site anslysis
23 days ago
Gordon Smyth
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0
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1
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287
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Comment:
Comment: Right way to pseudobulk donors across replicates in edgeR
23 days ago
Gordon Smyth
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0
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1
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586
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Comment:
Comment: Strange logFC values in differential methylation site anslysis
24 days ago
Gordon Smyth
50k
0
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1
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586
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Comment:
Comment: Strange logFC values in differential methylation site anslysis
24 days ago
Gordon Smyth
50k
0
votes
0
replies
171
views
Answer:
Answer: Different results from DGE using different subgroups in model.matrix
24 days ago
Gordon Smyth
50k
0
votes
0
replies
586
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Comment:
Comment: Strange logFC values in differential methylation site anslysis
25 days ago • updated 24 days ago
Gordon Smyth
50k
0
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1
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586
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Answer:
Answer: Strange logFC values in differential methylation site anslysis
25 days ago
Gordon Smyth
50k
2
votes
0
replies
337
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Answer:
Answer: DGE analysis with LIMMA
26 days ago
Gordon Smyth
50k
0
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0
replies
184
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Answer:
Answer: ExactTest vs QLFTest
28 days ago • updated 26 days ago
Gordon Smyth
50k
0
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1
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215
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Comment:
Comment: Interactions in batches of varying size with different number of replicates usin
29 days ago
Gordon Smyth
50k
0
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1
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215
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Comment:
Comment: Interactions in batches of varying size with different levels of replicates usin
29 days ago
Gordon Smyth
50k
0
votes
1
reply
211
views
Answer:
Answer: Differential enrichment analysis
29 days ago
Gordon Smyth
50k
0
votes
2
replies
586
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Comment:
Comment: Strange logFC values in differential methylation site anslysis
4 weeks ago
Gordon Smyth
50k
0
votes
0
replies
207
views
Answer:
Answer: Error in featureCounts matrix
4 weeks ago
Gordon Smyth
50k
1
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1
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381
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Comment:
Comment: Library size normalization in methylation count analysis
4 weeks ago
Gordon Smyth
50k
0
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1
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381
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Comment:
Comment: Library size normalization in methylation count analysis
4 weeks ago
Gordon Smyth
50k
0
votes
1
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381
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Answer:
Answer: Library size normalization in methylation count analysis
4 weeks ago
Gordon Smyth
50k
0
votes
2
replies
415
views
Comment:
Comment: limma fo continous variables
4 weeks ago
Gordon Smyth
50k
0
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1
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415
views
Comment:
Comment: limma fo continous variables
5 weeks ago
Gordon Smyth
50k
0
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1
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415
views
Answer:
Answer: limma fo continous variables
5 weeks ago
Gordon Smyth
50k
0
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1
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235
views
Answer:
Answer: limma model matrix questions
5 weeks ago
Gordon Smyth
50k
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