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Comment: Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
7 hours ago • updated 6 hours ago Gordon Smyth 47k
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73
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Comment: Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
9 hours ago • updated 8 hours ago Gordon Smyth 47k
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88
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Answer: Answer: Volcano Plot in R
2 days ago Gordon Smyth 47k
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862
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Answer: Answer: limma: decideTests
2 days ago Gordon Smyth 47k
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63
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Answer: Answer: NAs in some genes in topTable output
3 days ago • updated 2 days ago Gordon Smyth 47k
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45
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Answer: Answer: limma on spectral data
3 days ago Gordon Smyth 47k
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54
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Answer: Answer: Subset count data in DGEList using edgeR/DESeq2
3 days ago Gordon Smyth 47k
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126
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Comment: Comment: Processing data with voom "expression values" and "weights"
7 days ago Gordon Smyth 47k
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1.9k
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Comment: Comment: the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC
8 days ago • updated 7 days ago Gordon Smyth 47k
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95
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Answer: Answer: R: Confused about Limma R package output being LogFC or Log2FC
8 days ago • updated 7 days ago Gordon Smyth 47k
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126
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Answer: Answer: Processing data with voom "expression values" and "weights"
8 days ago • updated 7 days ago Gordon Smyth 47k
2
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92
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Answer: Answer: Help with the design matrix for longitudinal study
9 days ago Gordon Smyth 47k
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143
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Comment: Comment: Why is it better to count genes at the exon-level using subread::featureCounts()
15 days ago Gordon Smyth 47k
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143
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Answer: Answer: Why is it better to count genes at the exon-level using subread::featureCounts()
15 days ago Gordon Smyth 47k
0
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111
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Answer: Answer: Orange point meaning in plotSmear with edgeR
15 days ago Gordon Smyth 47k
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108
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Comment: Comment: Time series between two conditions with a common time zero
16 days ago Gordon Smyth 47k
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114
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Answer: Answer: Estimating Fold-Changes of Lowly Expressed Genes
17 days ago • updated 16 days ago Gordon Smyth 47k
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124
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Answer: Answer: Remove batch effect between microarray data
17 days ago Gordon Smyth 47k
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99
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Answer: Answer: Limma: how to make a table of logFC of certain genes (I need to define logFC of
19 days ago Gordon Smyth 47k
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164
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Comment: Comment: Bulk RNA seq with deseq2, rnaseqGene, or edgeR
21 days ago Gordon Smyth 47k
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135
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Answer: Answer: Differential gene expression analysis with data matrix generated with RSEM
22 days ago Gordon Smyth 47k
1
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151
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Comment: Comment: Limma repeated-measures model: Partial NA coefficients
22 days ago Gordon Smyth 47k
2
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151
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Answer: Answer: Limma repeated-measures model: Partial NA coefficients
24 days ago • updated 23 days ago Gordon Smyth 47k
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120
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Answer: Answer: Assigning the name of top 100 DE transcripts/genes to Volcano plot
27 days ago Gordon Smyth 47k
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99
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Comment: Comment: GSA type of input data
27 days ago Gordon Smyth 47k
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88
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Answer: Answer: Alternatives to Voom in experiments without replicate
27 days ago Gordon Smyth 47k
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83
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Answer: Answer: Extracting the tophits from limma Volcanoplot and issue with geneIDs
27 days ago Gordon Smyth 47k
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124
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Comment: Comment: Time series with two treatments including a common time zero
27 days ago • updated 16 days ago Gordon Smyth 47k
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0
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270
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Comment: Comment: Implementation of the "original" GSEA algorithm in R
27 days ago Gordon Smyth 47k
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1
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124
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Answer: Answer: Time series with two treatments including a common time zero
28 days ago Gordon Smyth 47k
2
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1
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197
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Comment: Comment: Create the design matrix
28 days ago Gordon Smyth 47k
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1
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197
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Answer: Answer: Create the design matrix
29 days ago Gordon Smyth 47k
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0
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1.3k
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Comment: Comment: limma vs t-test
4 weeks ago Gordon Smyth 47k
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168
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Answer: Answer: suggest to report differential estimate in edgeR
4 weeks ago Gordon Smyth 47k
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1
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279
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Comment: Comment: How to identify top most variable genes from log2 normalized data?
4 weeks ago Gordon Smyth 47k
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285
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Comment: Comment: What function in edgeR normalize the reads between samples?
4 weeks ago Gordon Smyth 47k
1
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1
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279
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Answer: Answer: How to identify top most variable genes from log2 normalized data?
4 weeks ago Gordon Smyth 47k
0
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1
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285
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Answer: Answer: What function in edgeR normalize the reads between samples?
4 weeks ago Gordon Smyth 47k
1
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0
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132
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Answer: Answer: Inccorect group number in DGEList
5 weeks ago Gordon Smyth 47k
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0
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201
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Answer: Answer: I need help with EdgeR!
5 weeks ago Gordon Smyth 47k
2
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0
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144
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Answer: Answer: limma: R-squared for time-series data
6 weeks ago Gordon Smyth 47k
1
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1
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251
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Answer: Answer: Question about making Contrasts for comparisons and assignment of values
6 weeks ago Gordon Smyth 47k
2
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1
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190
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Answer: Answer: limma plotMDS - logFC inverted?
6 weeks ago Gordon Smyth 47k
1
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0
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139
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Answer: Answer: Limma, Log2FC and pvalue changing depending on the order of the samples.
6 weeks ago Gordon Smyth 47k
1
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1
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235
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Comment: Comment: Question on creating right design matrix in edgeR
6 weeks ago Gordon Smyth 47k
1
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1
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235
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Answer: Answer: Question on creating right design matrix in edgeR
6 weeks ago Gordon Smyth 47k
1
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1
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235
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Answer: Answer: Question on creating right design matrix in edgeR
6 weeks ago Gordon Smyth 47k
1
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1
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270
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Comment: Comment: Implementation of the "original" GSEA algorithm in R
6 weeks ago Gordon Smyth 47k
0
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1
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294
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Comment: Comment: How to interpret Histogram of average log2 CPM filtering in EdgeR?
7 weeks ago Gordon Smyth 47k
2
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1
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294
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Comment: Comment: How to interpret Histogram of average log2 CPM filtering in EdgeR?
7 weeks ago Gordon Smyth 47k
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