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p-value
•
reset
0
votes
0
replies
265
views
DEqMS function "outputResult" reports wrong sca.adj.pval
outputresult
DEqMS
sca.adj.pval
error
p-value
7 months ago
Bastian
• 0
0
votes
1
reply
583
views
What does one-sided p-value in DESeq2 mean in biological terms?
one-sided
nbinomWaldTest
p-value
meta-analysis
DESeq2
updated 21 months ago by
Michael Love
40k • written 21 months ago by
nash12
• 0
1
vote
2
replies
3.0k
views
Why are my p-values deflated (GWAS)?
gwas
genesis
p-value
q-q-plot
updated 2.3 years ago by
Anna
• 0 • written 3.5 years ago by
solanum
• 0
7
votes
2
replies
1.3k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 23 months ago by
António Miguel de Jesus Domingues
▴ 490 • written 2.5 years ago by
Alexei Leliavski
▴ 60
4
votes
6
replies
792
views
Question about the usage of Package, qvalue
statistical significance
p-value
q-value
FDR
qvalue
3.4 years ago
manozawa
▴ 10
1
vote
2
replies
572
views
IHW scale of problem
ihw
p-value
multiple hypothesis
updated 4.0 years ago by
Wolfgang Huber
13k • written 4.0 years ago by
xiaotong.yao23
▴ 10
0
votes
1
reply
689
views
Dependence of FDR and P-values on sample size
edgeR
FDR
p-value
Benjamini-Hochberg
Differential Analysis
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
ilovesuperheroes1993
• 0
3
votes
12
replies
1.1k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
4.3 years ago
ariel
▴ 10
2
votes
2
replies
1.6k
views
One-sided p-value from DESeq2
DESeq2
nbinomWaldTest
one-sided
p-value
updated 4.8 years ago by
Michael Love
40k • written 4.8 years ago by
t.kuilman
170
0
votes
0
replies
757
views
Question: Problem for getting P-Value in Module-Trait Relationship in WGCNA
weighted correlation network analysis
WGCNA
P-Value
4.8 years ago
modarzi
▴ 10
40
votes
44
replies
8.6k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR
p-value
DESeq
RNA-Seq
updated 5.5 years ago by
Wade Davis
▴ 60 • written 6.1 years ago by
yjiangnan
▴ 10
0
votes
0
replies
734
views
Question: Enrichment heatmap - GOstats package of R
Gostats
p-value
5.9 years ago
salamandra
▴ 20
5
votes
6
replies
1.1k
views
pvalue of deseq2
deseq2
normalization
p-value
metaseq
updated 5.9 years ago by
Ryan C. Thompson
7.8k • written 5.9 years ago by
ed_isfahani
• 0
2
votes
5
replies
2.4k
views
Limma toptable interpretation check
limma
microarray
fdr
p-value
results
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
bhgyu
▴ 30
2
votes
1
reply
1.7k
views
DiffBind dba.analyze() to return all differentially enriched peaks?
diffbind
p-value
differential binding analysis
fold enrichment values using diffbind
updated 7.0 years ago by
Rory Stark
★ 4.9k • written 7.0 years ago by
alisonhanh.nguyen
• 0
10
votes
14
replies
11k
views
how DESeq calculates p-value ?
deseq
differential gene expression
statistics
p-value
updated 2.3 years ago by
Kai_Qi
▴ 20 • written 7.3 years ago by
Giard
▴ 30
11
votes
20
replies
3.5k
views
Detection p-value: difference between limma and lumi packages
p-value
detection
updated 7.4 years ago by
Gordon Smyth
47k • written 7.4 years ago by
Eleni Christodoulou
▴ 150
5
votes
2
replies
2.1k
views
RankProd: Why are p-values=0?
rankprod
p-value
updated 8.0 years ago by
James W. MacDonald
63k • written 8.0 years ago by
brilladine
• 0
1
vote
2
replies
1.9k
views
MEDIPS vs MACS: why does MEDIPS generate more conservative p-values
p-value
medips
MACS
updated 8.0 years ago by
Lukas Chavez
▴ 570 • written 8.0 years ago by
tptacek3050
• 0
19 results • Page
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Recent ...
Replies
Answer: multiple filters in biomaRt
by
RuBBiT0
▴ 10
First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro…
Comment: Diffbind "No genome detected"
by
kyliecode
• 0
Hi Dr. Stark, Thanks very much for your reply! The bam files were output from nf-core/chipseq pipeline and for some reason, they do not ha…
Answer: Discrepancy between DESeq2 files produced in Galaxy and R(RStudio)
by
Michael Love
40k
I guess that Galaxy may be using some kind of LFC shrinkage, but without seeing their code I wouldn't know for sure. Shrinkage generally…
Comment: TCGAbiolinks cannot find bcr_patient_barcode
by
Habil Zare
▴ 170
I checked your example with the devel version 2.29.6 on Bioc and it worked fine. Thanks for the fix!
Answer: error in ChAMP loading file
by
jenniferbrowngates
• 0
I got a lot of information from this website about different topics which is beneficial for me too so I thank this site and also suggest a …
Votes
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Comment: Error: biomaRt has encountered an unexpected server error.
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
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