73
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8
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65k
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conceptual question about FDR, FDR adjusted p-value and q-value
fdr qvalue
updated 9.3 years ago by 53k • written 13.1 years ago by ▴ 450
52
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20
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52k
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updated 9.6 years ago by • 0 • written 10.1 years ago by ▴ 110
44
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29
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updated 4.7 years ago by ▴ 130 • written 4.8 years ago by ▴ 160
41
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44
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14k
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Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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updated 8.1 years ago by ▴ 60 • written 8.7 years ago by ▴ 10
38
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23
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18k
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11.3 years ago • updated 10 months ago Michael Love 43k
34
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updated 16 months ago by 43k • written 10.8 years ago by ▴ 130
34
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updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 100
34
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written 12.1 years ago by ▴ 270
33
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21.3 years ago • updated 5.2 years ago Gordon Smyth 53k
32
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16
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22k
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difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
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updated 7.7 years ago by ▴ 20 • written 9.5 years ago by ▴ 200
31
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63k
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deseq2 filter the low counts
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28
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Effect of lfcThreshold on p-value in DESeq2
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updated 2.3 years ago by ▴ 10 • written 8.3 years ago by ▴ 40
28
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updated 8.4 years ago by 53k • written 10.8 years ago by ▴ 160
28
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updated 8.5 years ago by ▴ 10 • written 8.9 years ago by ▴ 100
28
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6
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48k
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DESeq2: Is it possible to convert read counts to expression values via TPM and return these values?
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updated 3.8 years ago by ▴ 20 • written 9.0 years ago by ▴ 60
28
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43
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11k
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Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
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updated 9.8 years ago by 25k • written 9.9 years ago by ▴ 80
27
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13
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20k
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problems about installation of package ‘Rhtslib’, ‘Rsamtools’ ,‘GenomicAlignments’ , ‘ShortRead’ on macOS Big Sur using R 4.1.0
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updated 3.0 years ago by • 0 • written 4.7 years ago by ▴ 60
27
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21
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26k
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updated 3.2 years ago by 68k • written 10.7 years ago by ▴ 60
27
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7
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Usability of ERCC spike-ins in standard RNAseq experiments
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updated 9.2 years ago by ★ 3.8k • written 9.2 years ago by ▴ 30
27
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17
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10k
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DESeq2 1.20.0 lfcshrink function
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updated 4.6 years ago by 43k • written 7.6 years ago by ▴ 50
27
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22
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23k
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DESeq2 for ChIP-seq differential peaks
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updated 8.5 years ago by ▴ 120 • written 10.4 years ago by ▴ 200
26
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7
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13k
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limma deseq2 edger rnaseq
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 20
25
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37
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17k
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Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq RSEM TCGA edgeR normalization
updated 9.0 years ago by 53k • written 9.0 years ago by ▴ 840
25
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11
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9.3k
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Normalization methodology in DESeq/DESeq2 vs edgeR
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updated 10.2 years ago by ★ 3.8k • written 10.2 years ago by ▴ 90
25
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9
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voom for spectral counts
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updated 11.0 years ago by 53k • written 11.0 years ago by ▴ 40
24
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11
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21k
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when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
limma voom limma voom rna-seq quantile normalization
updated 10.0 years ago by 53k • written 10.0 years ago by ▴ 50
24
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12
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14k
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updated 10.7 years ago by ▴ 20 • written 10.7 years ago by ▴ 370
23
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Bioconductor vs BioConductor
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updated 5.7 years ago by 53k • written 5.7 years ago by ▴ 40
22
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12
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New function lfcShrink() in DESeq2
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updated 6.4 years ago by • 0 • written 8.7 years ago by 43k
22
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10
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Error in GRanges: could not find symbol "recursive" in environment of the generic function
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updated 8.8 years ago by ▴ 10 • written 8.9 years ago by ▴ 80
22
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13
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gene dispersion, what does it mean?
gener rnaseq
updated 2.8 years ago by 53k • written 10.1 years ago by ▴ 80
22
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8
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Limma camera function never gives any differentially expressed gene sets
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updated 8.4 years ago by • 0 • written 10.5 years ago by ▴ 420
22
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4
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updated 10.7 years ago by 53k • written 10.7 years ago by ▴ 840
22
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15
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12k
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biomaRt error unable to fix: need help troubleshooting
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updated 2.2 years ago by ▴ 10 • written 3.8 years ago by ▴ 50
21
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5
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19k
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using duplicateCorrelation with limma+voom for RNA-seq data
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updated 10.7 years ago by 53k • written 11.7 years ago by ▴ 190
21
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1
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9.1k
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Differences between limma voom E values and edgeR cpm values?
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updated 11.3 years ago by 53k • written 11.6 years ago by ▴ 90
21
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13
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17k
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Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
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updated 11.2 years ago by 68k • written 11.2 years ago by ▴ 50
21
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10
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10k
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Tutorial: Bioconductor on Coursera
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updated 7.8 years ago by • 0 • written 10.4 years ago by ★ 6.5k
21
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24
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updated 9.7 years ago by ▴ 470 • written 10.2 years ago by ★ 2.1k
21
votes
34
replies
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Biomart error when updating to R 4.0.2
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updated 5.3 years ago by ★ 6.6k • written 5.3 years ago by ▴ 40
20
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Tutorial: Updated Support Site Editor
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updated 4 months ago by • 0 • written 7.0 years ago by 4.3k
20
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10
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22k
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How do I merge a list of GRanges?
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updated 4.0 years ago by ▴ 40 • written 9.6 years ago by ▴ 40
20
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13
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News: markdown is coming to the support site
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8.5 years ago • updated 7.9 years ago Lucas Schiffer ▴ 240
20
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18
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Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
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updated 10.3 years ago by ▴ 870 • written 10.3 years ago by ▴ 840
20
votes
10
replies
9.0k
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Correct sequence of functions for edgeR, edgeR robust and edgeR QL.
edger estimatedispersions glm
updated 9.9 years ago by 53k • written 9.9 years ago by ▴ 180
20
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15
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DESeq2 output explanation
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updated 4.2 years ago by 43k • written 11.2 years ago by ▴ 100
19
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7
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DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2 ensembl
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 170
19
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8
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How to check the read length for all the TCGA data samples in GDC?
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updated 7.8 years ago by 21k • written 7.8 years ago by ▴ 120
19
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6
replies
49k
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How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
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updated 9.3 years ago by ★ 6.8k • written 9.3 years ago by ▴ 70
19
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4
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Confidence intervals on edgeR logFC
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updated 9.8 years ago by • 0 • written 11.3 years ago by ▴ 40
46,723 results • Page 1 of 935
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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