Showing : fdr • reset
1
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1
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1.1k
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Weird distribution of p-values, with no significant adjusted p-values?
fdr limmaGUI p-values limma
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
7
votes
2
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2.6k
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False discovery rates in DEP
p-value FDR DEP
updated 3.8 years ago by ▴ 510 • written 4.3 years ago by ▴ 60
4
votes
6
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2.0k
views
Question about the usage of Package, qvalue
statistical significance p-value q-value FDR qvalue
5.2 years ago manozawa ▴ 10
2
votes
2
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4.0k
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How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 5.5 years ago by 52k • written 5.5 years ago by ▴ 10
1
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2
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2.4k
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FDR and mixed FDR in limma fry()
limma FDR
updated 5.8 years ago by 52k • written 5.8 years ago by • 0
0
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1
reply
1.8k
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Dependence of FDR and P-values on sample size
edgeR FDR p-value Benjamini-Hochberg Differential Analysis
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
2
votes
12
replies
2.2k
views
msmsTests, NA values in test.results output
Proteomics msmstests FDR
updated 6.4 years ago by 1.6k • written 6.4 years ago by • 0
3
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2
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5.8k
views
p.adjust function fdr and BH
fdr BH
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 10
3
votes
4
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2.5k
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Does Fold change cutoff changes the FDR value using glmTreat function in edgeR?
edgeR r bioconductor diffferential expression fdr
updated 6.8 years ago by 68k • written 6.8 years ago by ▴ 120
0
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6
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1.9k
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Defining subsets for FDR correction
fdr deseq2 ihw
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 30
41
votes
44
replies
12k
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Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 7.3 years ago by ▴ 60 • written 7.9 years ago by ▴ 10
12
votes
3
replies
12k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot limma fdr
7.7 years ago • updated 4.3 years ago tcalvo ▴ 100
0
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1
reply
1.3k
views
EdgeR dispersion and FDR
edger FDR rnaseq
updated 7.7 years ago by ★ 28k • written 7.7 years ago by • 0
2
votes
5
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4.1k
views
Limma toptable interpretation check
limma microarray fdr p-value results
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 30
0
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1
reply
1.5k
views
FUNCTIONAL ENRICHMENT ANALYSIS
genecodis3 fdr
updated 7.9 years ago by ★ 3.4k • written 7.9 years ago by ▴ 30
2
votes
2
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1.6k
views
fdr score for degs
fdr deg
updated 7.9 years ago by ▴ 840 • written 7.9 years ago by ▴ 30
1
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5
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3.6k
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Inspection and Correction of p-values in DESeq2 pipeline by Bernd
deseq2 FDR fdrtool
updated 8.0 years ago by ▴ 610 • written 8.1 years ago by ▴ 20
1
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1
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1.8k
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Question about testing main factors and doing FDR correction in a multiple-factor design in DESeq2.
deseq2 multiple factor design FDR fdrtool
updated 8.1 years ago by 43k • written 8.1 years ago by • 0
2
votes
2
replies
8.9k
views
edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR bioconductor fdr statistics differential gene expression
8.3 years ago jol.espinoz ▴ 40
0
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1
reply
1.7k
views
Change the FDR in DEXSeq
FDR padj
updated 8.4 years ago by ▴ 50 • written 8.4 years ago by • 0
69
votes
8
replies
61k
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conceptual question about FDR, FDR adjusted p-value and q-value
fdr qvalue
updated 8.5 years ago by 52k • written 12.3 years ago by ▴ 440
0
votes
2
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1.9k
views
DESeq with hierarchical FDR correction
deseq2 fdr
updated 9.6 years ago by 43k • written 9.6 years ago by • 0
2
votes
15
replies
3.7k
views
BiSeq trimClusters FDR.loc confusion
biseq fdr data results
10.0 years ago • updated 9.9 years ago mnaymik ▴ 10
3
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5
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2.2k
views
help! new to R! Detection p value cut off
p values microarray FDR
10.1 years ago a • 0
1
vote
4
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2.8k
views
strange FDR distribution for RNA-seq sample with edgeR
edgeR RNA-seq FDR
updated 10.3 years ago by 52k • written 10.3 years ago by ▴ 10
25 results • Page 1 of 1
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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Answer: Error in cnetplot by Guido Hooiveld ★ 4.1k
Unfortunately you did not show how you generated your input data (the object `enrichment`), nor did you show the output from `sessionInfo()…
Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k
I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…
Votes
Answer: Explannation for ROAST results
Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
A: Machine learning in R book
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