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Answer:
Answer: Design matrix Differential expression analysis
13 hours ago by
Gordon Smyth
★ 7.1k
0
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0
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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
1
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1
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395
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Answer:
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
7 days ago by
Gordon Smyth
★ 7.1k
0
votes
1
reply
260
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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
4
votes
1
reply
304
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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
1
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0
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287
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Answer:
Answer: Removing Illumina microarray probes with no expression HumanHT-12v4
14 days ago by
Gordon Smyth
★ 7.1k
2
votes
1
reply
401
views
Answer:
Answer: differential gene expression analysis when not all samples have an untreated cou
17 days ago by
Gordon Smyth
★ 7.1k
2
votes
0
replies
263
views
Answer:
Answer: Choosing an FC Threshold
5 weeks ago by
Gordon Smyth
★ 7.1k
0
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1
reply
479
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Answer:
Answer: 'Invalid parameter' error to generate a count matrix using featurecounts
6 weeks ago by
Gordon Smyth
★ 7.1k
3
votes
3
replies
454
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Answer:
Answer: Differential express genes in imbalance groups
6 weeks ago by
Gordon Smyth
★ 7.1k
1
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0
replies
674
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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
1
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0
replies
1.2k
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Answer:
Answer: MA graphs for EdgeR and Voom vary
8 weeks ago by
Gordon Smyth
★ 7.1k
2
votes
0
replies
726
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Answer:
Answer: Seeking Beginner-Friendly Resources for Deepening Understanding of Bioinformatic
8 weeks ago by
Gordon Smyth
★ 7.1k
1
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1
reply
468
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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
6
votes
1
reply
481
views
Answer:
Answer: Bayesian Differential Expression
11 weeks ago by
Gordon Smyth
★ 7.1k
1
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0
replies
923
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Answer:
Answer: EdgeR: upregulated with respect to what group?
3 months ago by
Gordon Smyth
★ 7.1k
0
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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
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0
replies
906
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
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Answer:
Answer: positive and negative Fold Change glmLRT test
3 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
746
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
3
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1
reply
494
views
Answer:
Answer: Differing p-value cutoffs of limma derived DEGs in volcanoplots
3 months ago by
Gordon Smyth
★ 7.1k
2
votes
1
reply
585
views
Answer:
Answer: Differential RNA editing using edgeR
3 months ago by
Gordon Smyth
★ 7.1k
1
vote
2
replies
1.6k
views
Answer:
Answer: how to test for differential expression in samples where a global increase in ge
4 months ago by
Gordon Smyth
★ 7.1k
2
votes
0
replies
1.6k
views
Answer:
Answer: Effect of Bootstrapping/Gibbs Sampling in Salmon Counts
4 months ago by
Gordon Smyth
★ 7.1k
3
votes
1
reply
690
views
Answer:
Answer: Microarray data analysis with and without contrast
6 months ago by
Gordon Smyth
★ 7.1k
1
vote
1
reply
6.7k
views
Answer:
Answer: Illumina HumanHT-12 V4.0 expression beadchip
6 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
1.5k
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Answer:
Answer: Laboratory Head Artificial Intelligence and Machine Learning (WEHI, Australia)
6 months ago by
Gordon Smyth
★ 7.1k
1
vote
1
reply
800
views
Answer:
Answer: Use limma for correlation analysis of RNA-seqdata and continous trait
7 months ago by
Gordon Smyth
★ 7.1k
2
votes
0
replies
2.1k
views
Answer:
Answer: Extracting Residuals from Differential Expression Model
8 months ago by
Gordon Smyth
★ 7.1k
1
vote
1
reply
610
views
Answer:
Answer: DGEList error in EdgeR - Warning: Error in $: $ operator is invalid for atomic v
9 months ago by
Gordon Smyth
★ 7.1k
0
votes
2
replies
1.1k
views
Answer:
Answer: Is RSEM required for RNA-seq data analysis using STAR and edgeR?
9 months ago by
Gordon Smyth
★ 7.1k
1
vote
0
replies
1.3k
views
Answer:
Answer: Comparing P-Values & FDR adjusted p-values between RNA-Seq experiments?
10 months ago by
Gordon Smyth
★ 7.1k
1
vote
1
reply
1.7k
views
Answer:
Answer: bar chart to show a p value of 0
10 months ago by
Gordon Smyth
★ 7.1k
2
votes
1
reply
2.4k
views
Answer:
Answer: How do I correctly format my limma/eBayes code?
10 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
1.4k
views
Answer:
Answer: How do I run DE for TPM values (not CPM)?
10 months ago by
Gordon Smyth
★ 7.1k
2
votes
1
reply
2.7k
views
Answer:
Answer: Limma returned only positive logFC values
11 months ago by
Gordon Smyth
★ 7.1k
2
votes
0
replies
815
views
Answer:
Answer: coef /makeContrasts very different results
11 months ago by
Gordon Smyth
★ 7.1k
1
vote
1
reply
1.0k
views
Answer:
Answer: Having problem on doing edgeR anlysis- cant create the DGE list through readbism
12 months ago by
Gordon Smyth
★ 7.1k
5
votes
1
reply
1.4k
views
Answer:
Answer: LIMMA: where to find the ANOVA?
12 months ago by
Gordon Smyth
★ 7.1k
2
votes
1
reply
3.7k
views
Answer:
Answer: edgeR, Pseudobulk scRNA-seq
12 months ago by
Gordon Smyth
★ 7.1k
0
votes
1
reply
609
views
Answer:
Answer: Is it possible to use limma to simultaneously analyze RNA-seq and gene expressio
12 months ago by
Gordon Smyth
★ 7.1k
8
votes
1
reply
4.5k
views
Answer:
Answer: What are the advantages of using the T2T as a reference vs GRCh38 today?
12 months ago by
Gordon Smyth
★ 7.1k
4
votes
1
reply
2.1k
views
Answer:
Answer: Limma: is it necessary to log-transform the data?
12 months ago by
Gordon Smyth
★ 7.1k
0
votes
0
replies
571
views
Answer:
Answer: "align" in rsubread only reading 1 out of 6 of my input files
13 months ago by
Gordon Smyth
★ 7.1k
4
votes
0
replies
1.1k
views
Answer:
Answer: RNA-seq analysis without replicates
13 months ago by
Gordon Smyth
★ 7.1k
7
votes
1
reply
976
views
Answer:
Answer: How to "guess" the transformation based on already-transformed, "normalized coun
13 months ago by
Gordon Smyth
★ 7.1k
3
votes
0
replies
629
views
Answer:
Answer: How to Merge RNA Replicates
13 months ago by
Gordon Smyth
★ 7.1k
2
votes
1
reply
796
views
Answer:
Answer: suprisingly high logFC using limma
13 months ago by
Gordon Smyth
★ 7.1k
3
votes
1
reply
1.4k
views
Answer:
Answer: extract gene coordinates and TSS from gene list
13 months ago by
Gordon Smyth
★ 7.1k
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