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FDR
•
reset
2
votes
15
replies
3.0k
views
BiSeq trimClusters FDR.loc confusion
biseq
fdr
data
results
9.0 years ago • updated 8.9 years ago
mnaymik
▴ 10
1
vote
4
replies
2.5k
views
strange FDR distribution for RNA-seq sample with edgeR
edgeR
RNA-seq
FDR
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
OLIVER, DAVID
▴ 10
40
votes
44
replies
10k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR
p-value
DESeq
RNA-Seq
updated 6.4 years ago by
Wade Davis
▴ 60 • written 6.9 years ago by
yjiangnan
▴ 10
67
votes
8
replies
55k
views
conceptual question about FDR, FDR adjusted p-value and q-value
fdr
qvalue
updated 7.5 years ago by
Gordon Smyth
50k • written 11.3 years ago by
Jack Luo
▴ 440
10
votes
3
replies
8.9k
views
Volcanoplot with limma - RAW P-values or Adj.P-Values
volcanoplot
limma
fdr
6.7 years ago • updated 3.4 years ago
tcalvo
▴ 90
1
vote
5
replies
3.1k
views
Inspection and Correction of p-values in DESeq2 pipeline by Bernd
deseq2
FDR
fdrtool
updated 7.1 years ago by
Bernd Klaus
▴ 610 • written 7.1 years ago by
deena
▴ 20
3
votes
5
replies
1.8k
views
help! new to R! Detection p value cut off
p values
microarray
FDR
9.1 years ago
a
• 0
2
votes
5
replies
3.1k
views
Limma toptable interpretation check
limma
microarray
fdr
p-value
results
updated 6.9 years ago by
Aaron Lun
★ 28k • written 6.9 years ago by
bhgyu
▴ 30
0
votes
1
reply
1.0k
views
EdgeR dispersion and FDR
edger
FDR
rnaseq
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
dsarbashis
• 0
0
votes
6
replies
1.5k
views
Defining subsets for FDR correction
fdr
deseq2
ihw
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
sven.schenk
▴ 20
3
votes
4
replies
2.1k
views
Does Fold change cutoff changes the FDR value using glmTreat function in edgeR?
edgeR
r
bioconductor
diffferential expression
fdr
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
Biologist
▴ 110
3
votes
2
replies
4.6k
views
p.adjust function fdr and BH
fdr
BH
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
zhang.jianhai
▴ 10
2
votes
12
replies
1.6k
views
msmsTests, NA values in test.results output
Proteomics
msmstests
FDR
updated 5.5 years ago by
Laurent Gatto
1.6k • written 5.5 years ago by
laural710
• 0
0
votes
1
reply
1.1k
views
Dependence of FDR and P-values on sample size
edgeR
FDR
p-value
Benjamini-Hochberg
Differential Analysis
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
ilovesuperheroes1993
• 0
1
vote
2
replies
1.8k
views
FDR and mixed FDR in limma fry()
limma
FDR
updated 4.9 years ago by
Gordon Smyth
50k • written 4.9 years ago by
Regeroka
• 0
2
votes
2
replies
2.8k
views
How adjusted p-values are calculated in limma
limma
r
transcriptomics
FDR
statistics
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
Wuschel
▴ 10
4
votes
6
replies
1.3k
views
Question about the usage of Package, qvalue
statistical significance
p-value
q-value
FDR
qvalue
4.3 years ago
manozawa
▴ 10
1
vote
1
reply
771
views
Weird distribution of p-values, with no significant adjusted p-values?
fdr
limmaGUI
p-values
limma
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
seahorsebox828
• 0
0
votes
2
replies
1.6k
views
DESeq with hierarchical FDR correction
deseq2
fdr
updated 8.7 years ago by
Michael Love
41k • written 8.7 years ago by
liam.philip.shaw
• 0
0
votes
1
reply
1.4k
views
Change the FDR in DEXSeq
FDR
padj
updated 7.5 years ago by
Jakub
▴ 50 • written 7.5 years ago by
arom2
• 0
2
votes
2
replies
7.6k
views
edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR
bioconductor
fdr
statistics
differential gene expression
7.4 years ago
jol.espinoz
▴ 40
1
vote
1
reply
1.5k
views
Question about testing main factors and doing FDR correction in a multiple-factor design in DESeq2.
deseq2
multiple factor design
FDR
fdrtool
updated 7.2 years ago by
Michael Love
41k • written 7.2 years ago by
marieke
• 0
2
votes
2
replies
1.3k
views
fdr score for degs
fdr
deg
updated 7.0 years ago by
svlachavas
▴ 830 • written 7.0 years ago by
nia
▴ 30
0
votes
1
reply
1.2k
views
FUNCTIONAL ENRICHMENT ANALYSIS
genecodis3
fdr
updated 7.0 years ago by
Robert Castelo
★ 3.2k • written 7.0 years ago by
nia
▴ 30
7
votes
2
replies
1.9k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 2.8 years ago by
António Miguel de Jesus Domingues
▴ 490 • written 3.4 years ago by
Alexei Leliavski
▴ 60
25 results • Page
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Answer: How to make DGEList and design matrix by edgeR package
by
Gordon Smyth
50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR
by
Gordon Smyth
50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
Answer: Log-cpm values from limma
by
Gordon Smyth
50k
The log-cpm values from voom() are not free of batch effect. If you want batch-corrected log-cpm values, we recommend cpm() followed by rem…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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