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