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P-Value
•
reset
0
votes
0
replies
535
views
DEqMS function "outputResult" reports wrong sca.adj.pval
outputresult
DEqMS
sca.adj.pval
error
p-value
18 months ago
Bastian
• 0
0
votes
1
reply
942
views
What does one-sided p-value in DESeq2 mean in biological terms?
one-sided
nbinomWaldTest
p-value
meta-analysis
DESeq2
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
nash12
• 0
1
vote
2
replies
4.0k
views
Why are my p-values deflated (GWAS)?
gwas
genesis
p-value
q-q-plot
updated 3.2 years ago by
Anna
• 0 • written 4.4 years ago by
solanum
• 0
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
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
2
replies
897
views
IHW scale of problem
ihw
p-value
multiple hypothesis
updated 4.9 years ago by
Wolfgang Huber
★ 13k • written 4.9 years ago by
xiaotong.yao23
▴ 10
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
3
votes
12
replies
1.6k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
5.2 years ago
ariel
▴ 20
2
votes
2
replies
2.0k
views
One-sided p-value from DESeq2
DESeq2
nbinomWaldTest
one-sided
p-value
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
t.kuilman
▴ 170
0
votes
0
replies
1.0k
views
Question: Problem for getting P-Value in Module-Trait Relationship in WGCNA
weighted correlation network analysis
WGCNA
P-Value
5.7 years ago
modarzi
▴ 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
0
votes
0
replies
968
views
Question: Enrichment heatmap - GOstats package of R
Gostats
p-value
6.8 years ago
salamandra
▴ 20
5
votes
6
replies
1.4k
views
pvalue of deseq2
deseq2
normalization
p-value
metaseq
updated 6.8 years ago by
Ryan C. Thompson
★ 7.9k • written 6.8 years ago by
ed_isfahani
• 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
2
votes
1
reply
2.0k
views
DiffBind dba.analyze() to return all differentially enriched peaks?
diffbind
p-value
differential binding analysis
fold enrichment values using diffbind
updated 7.9 years ago by
Rory Stark
★ 5.1k • written 7.9 years ago by
alisonhanh.nguyen
• 0
10
votes
14
replies
13k
views
how DESeq calculates p-value ?
deseq
differential gene expression
statistics
p-value
updated 3.1 years ago by
Kai_Qi
▴ 20 • written 8.2 years ago by
Giard
▴ 30
11
votes
20
replies
4.2k
views
Detection p-value: difference between limma and lumi packages
p-value
detection
updated 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
Eleni Christodoulou
▴ 150
5
votes
2
replies
2.3k
views
RankProd: Why are p-values=0?
rankprod
p-value
updated 8.8 years ago by
James W. MacDonald
65k • written 8.8 years ago by
brilladine
• 0
1
vote
2
replies
2.2k
views
MEDIPS vs MACS: why does MEDIPS generate more conservative p-values
p-value
medips
MACS
updated 8.9 years ago by
Lukas Chavez
▴ 570 • written 8.9 years ago by
tptacek3050
• 0
19 results • Page
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
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
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★ 3.2k
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shepherl
3.8k
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to
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▴ 30
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Gordon Smyth
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