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Answer: Answer: edgeR batch effect model matrix sanity check
8 hours ago by Gordon Smyth ★ 7.2k
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213
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Comment: Comment: Design model matrix with limma with cell different proportions estimates and bat
5 days ago by Gordon Smyth ★ 7.2k
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1.4k
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Answer: Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
17 days ago by Gordon Smyth ★ 7.2k
2
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0
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290
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Answer: Answer: RNAseq coverage vs depth for transcript isoform expression?
27 days ago by Gordon Smyth ★ 7.2k
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1
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311
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Answer: Answer: EdgeR - relationship between logFC and coefficients
5 weeks ago by Gordon Smyth ★ 7.2k
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549
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Comment: Comment: Design matrix Differential expression analysis
5 weeks ago by Gordon Smyth ★ 7.2k
2
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1
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549
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Answer: Answer: Design matrix Differential expression analysis
6 weeks ago by Gordon Smyth ★ 7.2k
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491
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Comment: Comment: Limma Analysis Agilent Microarray Data (GPL1708)
6 weeks ago by Gordon Smyth ★ 7.2k
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1.5k
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Answer: Answer: Differential Expression using Isoseq-supplemented reference transcriptome
6 weeks ago by Gordon Smyth ★ 7.2k
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491
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Answer: Answer: Limma Analysis Agilent Microarray Data (GPL1708)
7 weeks ago by Gordon Smyth ★ 7.2k
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330
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Answer: Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
7 weeks ago by Gordon Smyth ★ 7.2k
4
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1
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436
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Answer: Answer: How to use limma to find differentially expressed genes in response to a continu
7 weeks ago by Gordon Smyth ★ 7.2k
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314
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Comment: Comment: permutation test in edgeR
7 weeks ago by Gordon Smyth ★ 7.2k
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0
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474
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Comment: Comment: Difference when using difference number of pathways score to compare between 3 g
7 weeks ago by Gordon Smyth ★ 7.2k
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0
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324
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Answer: Answer: Removing Illumina microarray probes with no expression HumanHT-12v4
7 weeks ago by Gordon Smyth ★ 7.2k
2
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1
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477
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Answer: Answer: differential gene expression analysis when not all samples have an untreated cou
8 weeks ago by Gordon Smyth ★ 7.2k
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1
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468
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Comment: Comment: Limma compare between 3 conditions vs 2 conditions
8 weeks ago by Gordon Smyth ★ 7.2k
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0
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296
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Answer: Answer: Choosing an FC Threshold
11 weeks ago by Gordon Smyth ★ 7.2k
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0
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1.2k
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Comment: Comment: Shrink logFC values after edgeR
11 weeks ago by Gordon Smyth ★ 7.2k
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1
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543
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Comment: Comment: 'Invalid parameter' error to generate a count matrix using featurecounts
12 weeks ago by Gordon Smyth ★ 7.2k
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1
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543
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Answer: Answer: 'Invalid parameter' error to generate a count matrix using featurecounts
12 weeks ago by Gordon Smyth ★ 7.2k
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0
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531
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Comment: Comment: Differential express genes in imbalance groups
12 weeks ago by Gordon Smyth ★ 7.2k
3
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3
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531
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Answer: Answer: Differential express genes in imbalance groups
12 weeks ago by Gordon Smyth ★ 7.2k
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247
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Comment: Comment: Computing mid parent value for DE analysis
3 months ago by Gordon Smyth ★ 7.2k
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0
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810
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Answer: Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
3 months ago by Gordon Smyth ★ 7.2k
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0
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1.3k
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Answer: Answer: MA graphs for EdgeR and Voom vary
3 months ago by Gordon Smyth ★ 7.2k
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0
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1.2k
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Comment: Comment: Shrink logFC values after edgeR
3 months ago by Gordon Smyth ★ 7.2k
2
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0
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764
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Answer: Answer: Seeking Beginner-Friendly Resources for Deepening Understanding of Bioinformatic
3 months ago by Gordon Smyth ★ 7.2k
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0
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572
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Comment: Comment: Does the order of the batch variable matter in Limma design matrix?
3 months ago by Gordon Smyth ★ 7.2k
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0
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4.0k
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Comment: Comment: Can one plot % of variance using the plotMDS function?
3 months ago by Gordon Smyth ★ 7.2k
1
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1
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572
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Answer: Answer: Does the order of the batch variable matter in Limma design matrix?
12 weeks ago by Gordon Smyth ★ 7.2k
6
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1
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510
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Answer: Answer: Bayesian Differential Expression
3 months ago by Gordon Smyth ★ 7.2k
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0
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511
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Comment: Comment: filtering lowly expressed reads
4 months ago by Gordon Smyth ★ 7.2k
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0
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281
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Comment: Comment: Design matrix after RUVg correction
4 months ago by Gordon Smyth ★ 7.2k
2
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0
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3.0k
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Comment: Comment: Converting LogCPM to raw counts for DESEQ2
4 months ago by Gordon Smyth ★ 7.2k
1
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0
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990
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Answer: Answer: EdgeR: upregulated with respect to what group?
4 months ago by Gordon Smyth ★ 7.2k
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0
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1.4k
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Answer: Answer: Is there a program to average read counts from technical replicates?
4 months ago by Gordon Smyth ★ 7.2k
0
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0
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943
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Comment: Comment: How do I work out which condition the genes are down-regulated in?
4 months ago by Gordon Smyth ★ 7.2k
0
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0
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943
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Answer: Answer: How do I work out which condition the genes are down-regulated in?
4 months ago by Gordon Smyth ★ 7.2k
0
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0
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1.6k
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Answer: Answer: positive and negative Fold Change glmLRT test
4 months ago by Gordon Smyth ★ 7.2k
0
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0
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772
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Answer: Answer: logFoldChange computed by EdgeR different from naive log2FCcomputed based on rea
4 months ago by Gordon Smyth ★ 7.2k
2
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1
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1.2k
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Answer: Answer: Shrink logFC values after edgeR
4 months ago by Gordon Smyth ★ 7.2k
1
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1
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592
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Comment: Comment: Differing p-value cutoffs of limma derived DEGs in volcanoplots
4 months ago by Gordon Smyth ★ 7.2k
3
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1
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592
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Answer: Answer: Differing p-value cutoffs of limma derived DEGs in volcanoplots
4 months ago by Gordon Smyth ★ 7.2k
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0
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344
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Comment: Comment: Monotonic genes in results of differential gene expression analysis
4 months ago by Gordon Smyth ★ 7.2k
1
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0
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307
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Comment: Comment: Gene expression of microarray data
4 months ago by Gordon Smyth ★ 7.2k
0
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1
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658
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Comment: Comment: Differential RNA editing using edgeR
5 months ago by Gordon Smyth ★ 7.2k
2
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1
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658
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Answer: Answer: Differential RNA editing using edgeR
5 months ago by Gordon Smyth ★ 7.2k
0
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1
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615
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Comment: Comment: how to start DEG analysis after featurecounts
5 months ago by Gordon Smyth ★ 7.2k
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0
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1.8k
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Comment: Comment: how to test for differential expression in samples where a global increase in ge
6 weeks ago by Gordon Smyth ★ 7.2k
510 results • Page 1 of 11
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