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5
votes
1
reply
203
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Answer:
Answer: EdgeR - relationship between logFC and coefficients
2 days ago by
Gordon Smyth
★ 7.1k
1
vote
1
reply
430
views
Comment:
Comment: Design matrix Differential expression analysis
6 days ago by
Gordon Smyth
★ 7.1k
2
votes
1
reply
430
views
Answer:
Answer: Design matrix Differential expression analysis
9 days ago by
Gordon Smyth
★ 7.1k
0
votes
1
reply
425
views
Comment:
Comment: Limma Analysis Agilent Microarray Data (GPL1708)
13 days ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
1.3k
views
Answer:
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
14 days ago by
Gordon Smyth
★ 7.1k
1
vote
1
reply
425
views
Answer:
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
15 days ago by
Gordon Smyth
★ 7.1k
0
votes
1
reply
289
views
Answer:
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
16 days ago by
Gordon Smyth
★ 7.1k
4
votes
1
reply
337
views
Answer:
Answer: How to use limma to find differentially expressed genes in response to a continu
16 days ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
273
views
Comment:
Comment: permutation test in edgeR
20 days ago by
Gordon Smyth
★ 7.1k
1
vote
0
replies
447
views
Comment:
Comment: Difference when using difference number of pathways score to compare between 3 g
22 days ago by
Gordon Smyth
★ 7.1k
1
vote
0
replies
296
views
Answer:
Answer: Removing Illumina microarray probes with no expression HumanHT-12v4
22 days ago by
Gordon Smyth
★ 7.1k
2
votes
1
reply
417
views
Answer:
Answer: differential gene expression analysis when not all samples have an untreated cou
25 days ago by
Gordon Smyth
★ 7.1k
1
vote
1
reply
431
views
Comment:
Comment: Limma compare between 3 conditions vs 2 conditions
25 days ago by
Gordon Smyth
★ 7.1k
2
votes
0
replies
271
views
Answer:
Answer: Choosing an FC Threshold
6 weeks ago by
Gordon Smyth
★ 7.1k
1
vote
0
replies
1.1k
views
Comment:
Comment: Shrink logFC values after edgeR
7 weeks ago by
Gordon Smyth
★ 7.1k
0
votes
1
reply
490
views
Comment:
Comment: 'Invalid parameter' error to generate a count matrix using featurecounts
7 weeks ago by
Gordon Smyth
★ 7.1k
0
votes
1
reply
490
views
Answer:
Answer: 'Invalid parameter' error to generate a count matrix using featurecounts
7 weeks ago by
Gordon Smyth
★ 7.1k
1
vote
0
replies
464
views
Comment:
Comment: Differential express genes in imbalance groups
7 weeks ago by
Gordon Smyth
★ 7.1k
3
votes
3
replies
464
views
Answer:
Answer: Differential express genes in imbalance groups
7 weeks ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
222
views
Comment:
Comment: Computing mid parent value for DE analysis
9 weeks ago by
Gordon Smyth
★ 7.1k
1
vote
0
replies
698
views
Answer:
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
10 weeks ago by
Gordon Smyth
★ 7.1k
1
vote
0
replies
1.2k
views
Answer:
Answer: MA graphs for EdgeR and Voom vary
10 weeks ago by
Gordon Smyth
★ 7.1k
2
votes
0
replies
1.1k
views
Comment:
Comment: Shrink logFC values after edgeR
10 weeks ago by
Gordon Smyth
★ 7.1k
2
votes
0
replies
734
views
Answer:
Answer: Seeking Beginner-Friendly Resources for Deepening Understanding of Bioinformatic
10 weeks ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
486
views
Comment:
Comment: Does the order of the batch variable matter in Limma design matrix?
10 weeks ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
3.9k
views
Comment:
Comment: Can one plot % of variance using the plotMDS function?
10 weeks ago by
Gordon Smyth
★ 7.1k
1
vote
1
reply
486
views
Answer:
Answer: Does the order of the batch variable matter in Limma design matrix?
7 weeks ago by
Gordon Smyth
★ 7.1k
6
votes
1
reply
486
views
Answer:
Answer: Bayesian Differential Expression
12 weeks ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
466
views
Comment:
Comment: filtering lowly expressed reads
3 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
247
views
Comment:
Comment: Design matrix after RUVg correction
3 months ago by
Gordon Smyth
★ 7.1k
2
votes
0
replies
2.8k
views
Comment:
Comment: Converting LogCPM to raw counts for DESEQ2
3 months ago by
Gordon Smyth
★ 7.1k
1
vote
0
replies
931
views
Answer:
Answer: EdgeR: upregulated with respect to what group?
3 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
1.3k
views
Answer:
Answer: Is there a program to average read counts from technical replicates?
3 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
913
views
Comment:
Comment: How do I work out which condition the genes are down-regulated in?
3 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
913
views
Answer:
Answer: How do I work out which condition the genes are down-regulated in?
3 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
1.6k
views
Answer:
Answer: positive and negative Fold Change glmLRT test
3 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
752
views
Answer:
Answer: logFoldChange computed by EdgeR different from naive log2FCcomputed based on rea
3 months ago by
Gordon Smyth
★ 7.1k
2
votes
1
reply
1.1k
views
Answer:
Answer: Shrink logFC values after edgeR
3 months ago by
Gordon Smyth
★ 7.1k
1
vote
1
reply
502
views
Comment:
Comment: Differing p-value cutoffs of limma derived DEGs in volcanoplots
3 months ago by
Gordon Smyth
★ 7.1k
3
votes
1
reply
502
views
Answer:
Answer: Differing p-value cutoffs of limma derived DEGs in volcanoplots
3 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
312
views
Comment:
Comment: Monotonic genes in results of differential gene expression analysis
3 months ago by
Gordon Smyth
★ 7.1k
1
vote
0
replies
282
views
Comment:
Comment: Gene expression of microarray data
3 months ago by
Gordon Smyth
★ 7.1k
0
votes
1
reply
606
views
Comment:
Comment: Differential RNA editing using edgeR
4 months ago by
Gordon Smyth
★ 7.1k
2
votes
1
reply
606
views
Answer:
Answer: Differential RNA editing using edgeR
4 months ago by
Gordon Smyth
★ 7.1k
0
votes
1
reply
539
views
Comment:
Comment: how to start DEG analysis after featurecounts
4 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
1.6k
views
Comment:
Comment: how to test for differential expression in samples where a global increase in ge
8 days ago by
Gordon Smyth
★ 7.1k
0
votes
1
reply
1.6k
views
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
votes
0
replies
1.6k
views
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
votes
1
reply
1.6k
views
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
vote
0
replies
1.6k
views
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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