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Comment: Comment: Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
11 months ago by Gordon Smyth ★ 8.3k
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2.7k
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Answer: Answer: Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
11 months ago by Gordon Smyth ★ 8.3k
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3.5k
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Answer: Answer: How does edgeR's filterByExpr work?
11 months ago by Gordon Smyth ★ 8.3k
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3.5k
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Comment: Comment: How does edgeR's filterByExpr work?
11 months ago by Gordon Smyth ★ 8.3k
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1
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2.5k
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Comment: Comment: Does the order of the batch variable matter in Limma design matrix?
12 months ago by Gordon Smyth ★ 8.3k
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2.2k
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Comment: Comment: Kallisto: to scaledTPM or not to scaledTPM
12 months ago by Gordon Smyth ★ 8.3k
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2.2k
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Comment: Comment: Kallisto: to scaledTPM or not to scaledTPM
12 months ago by Gordon Smyth ★ 8.3k
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2
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2.2k
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Comment: Comment: Kallisto: to scaledTPM or not to scaledTPM
12 months ago by Gordon Smyth ★ 8.3k
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2.2k
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Answer: Answer: Kallisto: to scaledTPM or not to scaledTPM
12 months ago by Gordon Smyth ★ 8.3k
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0
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1.4k
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Comment: Comment: Seeking Advice on Using `edgeR` and `variancePartition` for RNA-seq Data with Mu
12 months ago by Gordon Smyth ★ 8.3k
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1.2k
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Comment: Comment: EdgeR gmlQLF with low number of genes
12 months ago by Gordon Smyth ★ 8.3k
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2
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1.2k
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Answer: Answer: EdgeR gmlQLF with low number of genes
13 months ago by Gordon Smyth ★ 8.3k
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2.0k
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Comment: Comment: gene expression normaliztion
13 months ago by Gordon Smyth ★ 8.3k
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1.2k
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Answer: Answer: Bulk RNA seq analysis on multiple conditions (4)
updated 13 months ago by 45k • written 14 months ago by ★ 8.3k
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1.2k
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Comment: Comment: Pathway analysis for DGEList
14 months ago by Gordon Smyth ★ 8.3k
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1.4k
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Comment: Comment: Adjusting for covariates such as duration of diabetes, age, sex and BMI
14 months ago by Gordon Smyth ★ 8.3k
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2.0k
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Answer: Answer: gene expression normaliztion
14 months ago by Gordon Smyth ★ 8.3k
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1
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866
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Answer: Answer: edgeR batch effect model matrix sanity check
15 months ago by Gordon Smyth ★ 8.3k
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721
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Comment: Comment: Design model matrix with limma with cell different proportions estimates and bat
15 months ago by Gordon Smyth ★ 8.3k
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3.0k
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Answer: Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
15 months ago by Gordon Smyth ★ 8.3k
2
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728
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Answer: Answer: RNAseq coverage vs depth for transcript isoform expression?
16 months ago by Gordon Smyth ★ 8.3k
5
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1
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954
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Answer: Answer: EdgeR - relationship between logFC and coefficients
16 months ago by Gordon Smyth ★ 8.3k
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1
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1.3k
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Comment: Comment: Design matrix Differential expression analysis
16 months ago by Gordon Smyth ★ 8.3k
2
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1
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1.3k
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Answer: Answer: Design matrix Differential expression analysis
16 months ago by Gordon Smyth ★ 8.3k
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1
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1.3k
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Comment: Comment: Limma Analysis Agilent Microarray Data (GPL1708)
16 months ago by Gordon Smyth ★ 8.3k
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3.1k
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Answer: Answer: Differential Expression using Isoseq-supplemented reference transcriptome
16 months ago by Gordon Smyth ★ 8.3k
1
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1
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1.3k
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Answer: Answer: Limma Analysis Agilent Microarray Data (GPL1708)
16 months ago by Gordon Smyth ★ 8.3k
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1
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1.0k
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Answer: Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
16 months ago by Gordon Smyth ★ 8.3k
4
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1
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1.5k
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Answer: Answer: How to use limma to find differentially expressed genes in response to a continu
16 months ago by Gordon Smyth ★ 8.3k
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0
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936
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Comment: Comment: permutation test in edgeR
16 months ago by Gordon Smyth ★ 8.3k
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0
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882
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Comment: Comment: Difference when using difference number of pathways score to compare between 3 g
17 months ago by Gordon Smyth ★ 8.3k
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0
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731
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Answer: Answer: Removing Illumina microarray probes with no expression HumanHT-12v4
17 months ago by Gordon Smyth ★ 8.3k
2
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1
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1.1k
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Answer: Answer: differential gene expression analysis when not all samples have an untreated cou
17 months ago by Gordon Smyth ★ 8.3k
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1
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1.0k
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Comment: Comment: Limma compare between 3 conditions vs 2 conditions
17 months ago by Gordon Smyth ★ 8.3k
2
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0
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767
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Answer: Answer: Choosing an FC Threshold
17 months ago by Gordon Smyth ★ 8.3k
1
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0
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3.1k
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Comment: Comment: Shrink logFC values after edgeR
17 months ago by Gordon Smyth ★ 8.3k
0
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1
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1.8k
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Comment: Comment: 'Invalid parameter' error to generate a count matrix using featurecounts
18 months ago by Gordon Smyth ★ 8.3k
0
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1
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1.8k
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Answer: Answer: 'Invalid parameter' error to generate a count matrix using featurecounts
18 months ago by Gordon Smyth ★ 8.3k
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0
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1.5k
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Comment: Comment: Differential express genes in imbalance groups
18 months ago by Gordon Smyth ★ 8.3k
3
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3
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1.5k
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Answer: Answer: Differential express genes in imbalance groups
18 months ago by Gordon Smyth ★ 8.3k
0
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0
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604
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Comment: Comment: Computing mid parent value for DE analysis
18 months ago by Gordon Smyth ★ 8.3k
1
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0
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2.0k
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Answer: Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
18 months ago by Gordon Smyth ★ 8.3k
1
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0
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2.1k
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Answer: Answer: MA graphs for EdgeR and Voom vary
18 months ago by Gordon Smyth ★ 8.3k
3
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0
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3.1k
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Comment: Comment: Shrink logFC values after edgeR
18 months ago by Gordon Smyth ★ 8.3k
2
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0
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1.4k
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Answer: Answer: Seeking Beginner-Friendly Resources for Deepening Understanding of Bioinformatic
18 months ago by Gordon Smyth ★ 8.3k
0
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0
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2.5k
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Comment: Comment: Does the order of the batch variable matter in Limma design matrix?
18 months ago by Gordon Smyth ★ 8.3k
0
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0
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5.1k
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Comment: Comment: Can one plot % of variance using the plotMDS function?
18 months ago by Gordon Smyth ★ 8.3k
1
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1
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2.5k
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Answer: Answer: Does the order of the batch variable matter in Limma design matrix?
11 months ago by Gordon Smyth ★ 8.3k
6
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1
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1.0k
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Answer: Answer: Bayesian Differential Expression
19 months ago by Gordon Smyth ★ 8.3k
0
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0
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1.1k
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Comment: Comment: filtering lowly expressed reads
19 months ago by Gordon Smyth ★ 8.3k
577 results • Page 2 of 12
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