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Answer: Answer: Differential Expression using Isoseq-supplemented reference transcriptome
3 days ago by Gordon Smyth ★ 7.1k
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378
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Answer: Answer: Limma Analysis Agilent Microarray Data (GPL1708)
5 days ago by Gordon Smyth ★ 7.1k
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1
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251
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Answer: Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
5 days ago by Gordon Smyth ★ 7.1k
4
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1
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293
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Answer: Answer: How to use limma to find differentially expressed genes in response to a continu
5 days ago by Gordon Smyth ★ 7.1k
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0
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270
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Answer: Answer: Removing Illumina microarray probes with no expression HumanHT-12v4
12 days ago by Gordon Smyth ★ 7.1k
2
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1
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396
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Answer: Answer: differential gene expression analysis when not all samples have an untreated cou
15 days ago by Gordon Smyth ★ 7.1k
2
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0
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263
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Answer: Answer: Choosing an FC Threshold
5 weeks ago by Gordon Smyth ★ 7.1k
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1
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475
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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
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3
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449
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Answer: Answer: Differential express genes in imbalance groups
6 weeks ago by Gordon Smyth ★ 7.1k
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0
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665
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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
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0
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1.2k
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Answer: Answer: MA graphs for EdgeR and Voom vary
8 weeks ago by Gordon Smyth ★ 7.1k
2
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0
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726
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Answer: Answer: Seeking Beginner-Friendly Resources for Deepening Understanding of Bioinformatic
8 weeks ago by Gordon Smyth ★ 7.1k
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1
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465
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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
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1
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480
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Answer: Answer: Bayesian Differential Expression
10 weeks ago by Gordon Smyth ★ 7.1k
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0
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919
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Answer: Answer: EdgeR: upregulated with respect to what group?
12 weeks ago by Gordon Smyth ★ 7.1k
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1.3k
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Answer: Answer: Is there a program to average read counts from technical replicates?
12 weeks ago by Gordon Smyth ★ 7.1k
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0
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904
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Answer: Answer: How do I work out which condition the genes are down-regulated in?
12 weeks ago by Gordon Smyth ★ 7.1k
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0
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1.6k
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Answer: Answer: positive and negative Fold Change glmLRT test
12 weeks ago by Gordon Smyth ★ 7.1k
0
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0
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742
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Answer: Answer: logFoldChange computed by EdgeR different from naive log2FCcomputed based on rea
12 weeks ago by Gordon Smyth ★ 7.1k
2
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1
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1.0k
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Answer: Answer: Shrink logFC values after edgeR
12 weeks ago by Gordon Smyth ★ 7.1k
3
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1
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488
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Answer: Answer: Differing p-value cutoffs of limma derived DEGs in volcanoplots
3 months ago by Gordon Smyth ★ 7.1k
2
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1
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578
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Answer: Answer: Differential RNA editing using edgeR
3 months ago by Gordon Smyth ★ 7.1k
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2
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1.6k
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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
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0
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1.6k
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Answer: Answer: Effect of Bootstrapping/Gibbs Sampling in Salmon Counts
4 months ago by Gordon Smyth ★ 7.1k
3
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1
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683
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Answer: Answer: Microarray data analysis with and without contrast
5 months ago by Gordon Smyth ★ 7.1k
1
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1
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6.7k
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Answer: Answer: Illumina HumanHT-12 V4.0 expression beadchip
6 months ago by Gordon Smyth ★ 7.1k
0
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0
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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
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1
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796
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Answer: Answer: Use limma for correlation analysis of RNA-seqdata and continous trait
7 months ago by Gordon Smyth ★ 7.1k
2
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0
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2.1k
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Answer: Answer: Extracting Residuals from Differential Expression Model
7 months ago by Gordon Smyth ★ 7.1k
1
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1
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607
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Answer: Answer: DGEList error in EdgeR - Warning: Error in $: $ operator is invalid for atomic v
9 months ago by Gordon Smyth ★ 7.1k
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2
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1.1k
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Answer: Answer: Is RSEM required for RNA-seq data analysis using STAR and edgeR?
9 months ago by Gordon Smyth ★ 7.1k
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0
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1.3k
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Answer: Answer: Comparing P-Values & FDR adjusted p-values between RNA-Seq experiments?
10 months ago by Gordon Smyth ★ 7.1k
1
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1
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1.7k
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Answer: Answer: bar chart to show a p value of 0
10 months ago by Gordon Smyth ★ 7.1k
2
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1
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2.4k
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Answer: Answer: How do I correctly format my limma/eBayes code?
10 months ago by Gordon Smyth ★ 7.1k
0
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0
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1.4k
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Answer: Answer: How do I run DE for TPM values (not CPM)?
10 months ago by Gordon Smyth ★ 7.1k
2
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1
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2.7k
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Answer: Answer: Limma returned only positive logFC values
10 months ago by Gordon Smyth ★ 7.1k
2
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0
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814
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Answer: Answer: coef /makeContrasts very different results
11 months ago by Gordon Smyth ★ 7.1k
1
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1
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1.0k
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Answer: Answer: Having problem on doing edgeR anlysis- cant create the DGE list through readbism
12 months ago by Gordon Smyth ★ 7.1k
5
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1
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1.4k
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Answer: Answer: LIMMA: where to find the ANOVA?
12 months ago by Gordon Smyth ★ 7.1k
2
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1
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3.7k
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Answer: Answer: edgeR, Pseudobulk scRNA-seq
12 months ago by Gordon Smyth ★ 7.1k
0
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1
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607
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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
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1
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4.5k
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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
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1
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2.1k
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Answer: Answer: Limma: is it necessary to log-transform the data?
12 months ago by Gordon Smyth ★ 7.1k
0
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0
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571
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Answer: Answer: "align" in rsubread only reading 1 out of 6 of my input files
13 months ago by Gordon Smyth ★ 7.1k
4
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0
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1.1k
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Answer: Answer: RNA-seq analysis without replicates
13 months ago by Gordon Smyth ★ 7.1k
7
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1
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973
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Answer: Answer: How to "guess" the transformation based on already-transformed, "normalized coun
13 months ago by Gordon Smyth ★ 7.1k
3
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0
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629
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Answer: Answer: How to Merge RNA Replicates
13 months ago by Gordon Smyth ★ 7.1k
2
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1
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794
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Answer: Answer: suprisingly high logFC using limma
13 months ago by Gordon Smyth ★ 7.1k
3
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1
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1.4k
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Answer: Answer: extract gene coordinates and TSS from gene list
13 months ago by Gordon Smyth ★ 7.1k
1
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1
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1.5k
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Answer: Answer: How to remove unknown batch-batch effects from GEO datasets
13 months ago by Gordon Smyth ★ 7.1k
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