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2
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1
reply
198
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Answer:
Answer: edgeR batch effect model matrix sanity check
1 day ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
215
views
Comment:
Comment: Design model matrix with limma with cell different proportions estimates and bat
6 days ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
1.4k
views
Answer:
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
18 days ago by
Gordon Smyth
★ 7.2k
2
votes
0
replies
291
views
Answer:
Answer: RNAseq coverage vs depth for transcript isoform expression?
28 days ago by
Gordon Smyth
★ 7.2k
5
votes
1
reply
311
views
Answer:
Answer: EdgeR - relationship between logFC and coefficients
5 weeks ago by
Gordon Smyth
★ 7.2k
1
vote
1
reply
550
views
Comment:
Comment: Design matrix Differential expression analysis
5 weeks ago by
Gordon Smyth
★ 7.2k
2
votes
1
reply
550
views
Answer:
Answer: Design matrix Differential expression analysis
6 weeks ago by
Gordon Smyth
★ 7.2k
0
votes
1
reply
493
views
Comment:
Comment: Limma Analysis Agilent Microarray Data (GPL1708)
6 weeks ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
1.5k
views
Answer:
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
6 weeks ago by
Gordon Smyth
★ 7.2k
1
vote
1
reply
493
views
Answer:
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
7 weeks ago by
Gordon Smyth
★ 7.2k
0
votes
1
reply
331
views
Answer:
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
7 weeks ago by
Gordon Smyth
★ 7.2k
4
votes
1
reply
437
views
Answer:
Answer: How to use limma to find differentially expressed genes in response to a continu
7 weeks ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
315
views
Comment:
Comment: permutation test in edgeR
7 weeks ago by
Gordon Smyth
★ 7.2k
1
vote
0
replies
475
views
Comment:
Comment: Difference when using difference number of pathways score to compare between 3 g
8 weeks ago by
Gordon Smyth
★ 7.2k
1
vote
0
replies
324
views
Answer:
Answer: Removing Illumina microarray probes with no expression HumanHT-12v4
8 weeks ago by
Gordon Smyth
★ 7.2k
2
votes
1
reply
478
views
Answer:
Answer: differential gene expression analysis when not all samples have an untreated cou
8 weeks ago by
Gordon Smyth
★ 7.2k
1
vote
1
reply
470
views
Comment:
Comment: Limma compare between 3 conditions vs 2 conditions
8 weeks ago by
Gordon Smyth
★ 7.2k
2
votes
0
replies
297
views
Answer:
Answer: Choosing an FC Threshold
11 weeks ago by
Gordon Smyth
★ 7.2k
1
vote
0
replies
1.2k
views
Comment:
Comment: Shrink logFC values after edgeR
12 weeks ago by
Gordon Smyth
★ 7.2k
0
votes
1
reply
543
views
Comment:
Comment: 'Invalid parameter' error to generate a count matrix using featurecounts
12 weeks ago by
Gordon Smyth
★ 7.2k
0
votes
1
reply
543
views
Answer:
Answer: 'Invalid parameter' error to generate a count matrix using featurecounts
12 weeks ago by
Gordon Smyth
★ 7.2k
1
vote
0
replies
533
views
Comment:
Comment: Differential express genes in imbalance groups
12 weeks ago by
Gordon Smyth
★ 7.2k
3
votes
3
replies
533
views
Answer:
Answer: Differential express genes in imbalance groups
12 weeks ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
248
views
Comment:
Comment: Computing mid parent value for DE analysis
3 months ago by
Gordon Smyth
★ 7.2k
1
vote
0
replies
814
views
Answer:
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
3 months ago by
Gordon Smyth
★ 7.2k
1
vote
0
replies
1.3k
views
Answer:
Answer: MA graphs for EdgeR and Voom vary
3 months ago by
Gordon Smyth
★ 7.2k
2
votes
0
replies
1.2k
views
Comment:
Comment: Shrink logFC values after edgeR
3 months ago by
Gordon Smyth
★ 7.2k
2
votes
0
replies
765
views
Answer:
Answer: Seeking Beginner-Friendly Resources for Deepening Understanding of Bioinformatic
3 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
573
views
Comment:
Comment: Does the order of the batch variable matter in Limma design matrix?
3 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
4.0k
views
Comment:
Comment: Can one plot % of variance using the plotMDS function?
3 months ago by
Gordon Smyth
★ 7.2k
1
vote
1
reply
573
views
Answer:
Answer: Does the order of the batch variable matter in Limma design matrix?
12 weeks ago by
Gordon Smyth
★ 7.2k
6
votes
1
reply
510
views
Answer:
Answer: Bayesian Differential Expression
4 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
512
views
Comment:
Comment: filtering lowly expressed reads
4 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
281
views
Comment:
Comment: Design matrix after RUVg correction
4 months ago by
Gordon Smyth
★ 7.2k
2
votes
0
replies
3.0k
views
Comment:
Comment: Converting LogCPM to raw counts for DESEQ2
4 months ago by
Gordon Smyth
★ 7.2k
1
vote
0
replies
991
views
Answer:
Answer: EdgeR: upregulated with respect to what group?
4 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
1.4k
views
Answer:
Answer: Is there a program to average read counts from technical replicates?
4 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
943
views
Comment:
Comment: How do I work out which condition the genes are down-regulated in?
4 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
943
views
Answer:
Answer: How do I work out which condition the genes are down-regulated in?
4 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
1.7k
views
Answer:
Answer: positive and negative Fold Change glmLRT test
4 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
772
views
Answer:
Answer: logFoldChange computed by EdgeR different from naive log2FCcomputed based on rea
4 months ago by
Gordon Smyth
★ 7.2k
2
votes
1
reply
1.2k
views
Answer:
Answer: Shrink logFC values after edgeR
4 months ago by
Gordon Smyth
★ 7.2k
1
vote
1
reply
592
views
Comment:
Comment: Differing p-value cutoffs of limma derived DEGs in volcanoplots
4 months ago by
Gordon Smyth
★ 7.2k
3
votes
1
reply
592
views
Answer:
Answer: Differing p-value cutoffs of limma derived DEGs in volcanoplots
4 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
344
views
Comment:
Comment: Monotonic genes in results of differential gene expression analysis
4 months ago by
Gordon Smyth
★ 7.2k
1
vote
0
replies
308
views
Comment:
Comment: Gene expression of microarray data
4 months ago by
Gordon Smyth
★ 7.2k
0
votes
1
reply
658
views
Comment:
Comment: Differential RNA editing using edgeR
5 months ago by
Gordon Smyth
★ 7.2k
2
votes
1
reply
658
views
Answer:
Answer: Differential RNA editing using edgeR
5 months ago by
Gordon Smyth
★ 7.2k
0
votes
1
reply
615
views
Comment:
Comment: how to start DEG analysis after featurecounts
5 months ago by
Gordon Smyth
★ 7.2k
0
votes
0
replies
1.8k
views
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
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