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Answer: Answer: Design matrix Differential expression analysis
4 hours ago by Gordon Smyth ★ 7.1k
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394
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Comment: Comment: Limma Analysis Agilent Microarray Data (GPL1708)
4 days ago by Gordon Smyth ★ 7.1k
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1.3k
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Answer: Answer: Differential Expression using Isoseq-supplemented reference transcriptome
5 days ago by Gordon Smyth ★ 7.1k
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394
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Answer: Answer: Limma Analysis Agilent Microarray Data (GPL1708)
7 days ago by Gordon Smyth ★ 7.1k
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259
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Answer: Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
7 days ago by Gordon Smyth ★ 7.1k
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1
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302
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Answer: Answer: How to use limma to find differentially expressed genes in response to a continu
7 days ago by Gordon Smyth ★ 7.1k
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256
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Comment: Comment: permutation test in edgeR
12 days ago by Gordon Smyth ★ 7.1k
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439
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Comment: Comment: Difference when using difference number of pathways score to compare between 3 g
13 days ago by Gordon Smyth ★ 7.1k
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287
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Answer: Answer: Removing Illumina microarray probes with no expression HumanHT-12v4
13 days ago by Gordon Smyth ★ 7.1k
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1
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401
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Answer: Answer: differential gene expression analysis when not all samples have an untreated cou
16 days ago by Gordon Smyth ★ 7.1k
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426
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Comment: Comment: Limma compare between 3 conditions vs 2 conditions
17 days ago by Gordon Smyth ★ 7.1k
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263
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Answer: Answer: Choosing an FC Threshold
5 weeks ago by Gordon Smyth ★ 7.1k
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1.1k
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Comment: Comment: Shrink logFC values after edgeR
5 weeks ago by Gordon Smyth ★ 7.1k
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1
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478
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Comment: Comment: 'Invalid parameter' error to generate a count matrix using featurecounts
6 weeks ago by Gordon Smyth ★ 7.1k
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1
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478
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Answer: Answer: 'Invalid parameter' error to generate a count matrix using featurecounts
6 weeks ago by Gordon Smyth ★ 7.1k
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451
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Comment: Comment: Differential express genes in imbalance groups
6 weeks ago by Gordon Smyth ★ 7.1k
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3
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451
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Answer: Answer: Differential express genes in imbalance groups
6 weeks ago by Gordon Smyth ★ 7.1k
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218
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Comment: Comment: Computing mid parent value for DE analysis
8 weeks ago by Gordon Smyth ★ 7.1k
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673
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Answer: Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
8 weeks ago by Gordon Smyth ★ 7.1k
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0
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1.2k
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Answer: Answer: MA graphs for EdgeR and Voom vary
8 weeks ago by Gordon Smyth ★ 7.1k
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0
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1.1k
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Comment: Comment: Shrink logFC values after edgeR
8 weeks ago by Gordon Smyth ★ 7.1k
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726
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Answer: Answer: Seeking Beginner-Friendly Resources for Deepening Understanding of Bioinformatic
8 weeks ago by Gordon Smyth ★ 7.1k
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466
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Comment: Comment: Does the order of the batch variable matter in Limma design matrix?
9 weeks ago by Gordon Smyth ★ 7.1k
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3.8k
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Comment: Comment: Can one plot % of variance using the plotMDS function?
9 weeks ago by Gordon Smyth ★ 7.1k
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466
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Answer: Answer: Does the order of the batch variable matter in Limma design matrix?
6 weeks ago by Gordon Smyth ★ 7.1k
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1
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481
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Answer: Answer: Bayesian Differential Expression
11 weeks ago by Gordon Smyth ★ 7.1k
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455
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Comment: Comment: filtering lowly expressed reads
12 weeks ago by Gordon Smyth ★ 7.1k
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0
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239
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Comment: Comment: Design matrix after RUVg correction
12 weeks ago by Gordon Smyth ★ 7.1k
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2.8k
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Comment: Comment: Converting LogCPM to raw counts for DESEQ2
12 weeks ago by Gordon Smyth ★ 7.1k
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0
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921
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Answer: Answer: EdgeR: upregulated with respect to what group?
3 months ago by Gordon Smyth ★ 7.1k
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1.3k
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Answer: Answer: Is there a program to average read counts from technical replicates?
3 months ago by Gordon Smyth ★ 7.1k
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905
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Comment: Comment: How do I work out which condition the genes are down-regulated in?
3 months ago by Gordon Smyth ★ 7.1k
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0
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905
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Answer: Answer: How do I work out which condition the genes are down-regulated in?
3 months ago by Gordon Smyth ★ 7.1k
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0
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1.6k
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Answer: Answer: positive and negative Fold Change glmLRT test
3 months ago by Gordon Smyth ★ 7.1k
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0
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745
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Answer: Answer: logFoldChange computed by EdgeR different from naive log2FCcomputed based on rea
3 months ago by Gordon Smyth ★ 7.1k
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1
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1.1k
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Answer: Answer: Shrink logFC values after edgeR
3 months ago by Gordon Smyth ★ 7.1k
1
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1
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493
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Comment: Comment: Differing p-value cutoffs of limma derived DEGs in volcanoplots
3 months ago by Gordon Smyth ★ 7.1k
3
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1
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493
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Answer: Answer: Differing p-value cutoffs of limma derived DEGs in volcanoplots
3 months ago by Gordon Smyth ★ 7.1k
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0
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307
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Comment: Comment: Monotonic genes in results of differential gene expression analysis
3 months ago by Gordon Smyth ★ 7.1k
1
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0
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277
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Comment: Comment: Gene expression of microarray data
3 months ago by Gordon Smyth ★ 7.1k
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1
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584
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Comment: Comment: Differential RNA editing using edgeR
3 months ago by Gordon Smyth ★ 7.1k
2
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1
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584
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Answer: Answer: Differential RNA editing using edgeR
3 months ago by Gordon Smyth ★ 7.1k
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1
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517
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Comment: Comment: how to start DEG analysis after featurecounts
3 months ago by Gordon Smyth ★ 7.1k
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0
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1.6k
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Comment: Comment: how to test for differential expression in samples where a global increase in ge
2 hours ago by Gordon Smyth ★ 7.1k
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1
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1.6k
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Comment: Comment: how to test for differential expression in samples where a global increase in ge
4 months ago by Gordon Smyth ★ 7.1k
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0
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1.6k
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Comment: Comment: how to test for differential expression in samples where a global increase in ge
4 months ago by Gordon Smyth ★ 7.1k
0
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1
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1.6k
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Comment: Comment: how to test for differential expression in samples where a global increase in ge
4 months ago by Gordon Smyth ★ 7.1k
1
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0
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1.6k
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Comment: Comment: how to test for differential expression in samples where a global increase in ge
4 months ago by Gordon Smyth ★ 7.1k
1
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1
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1.6k
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Comment: Comment: how to test for differential expression in samples where a global increase in ge
4 months ago by Gordon Smyth ★ 7.1k
1
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2
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1.6k
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Answer: Answer: how to test for differential expression in samples where a global increase in ge
4 months ago by Gordon Smyth ★ 7.1k
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