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p-value
•
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0
votes
0
replies
579
views
DEqMS function "outputResult" reports wrong sca.adj.pval
outputresult
DEqMS
sca.adj.pval
error
p-value
19 months ago
Bastian
• 0
0
votes
1
reply
968
views
What does one-sided p-value in DESeq2 mean in biological terms?
one-sided
nbinomWaldTest
p-value
meta-analysis
DESeq2
updated 2.7 years ago by
Michael Love
42k • written 2.7 years ago by
nash12
• 0
1
vote
2
replies
4.1k
views
Why are my p-values deflated (GWAS)?
gwas
genesis
p-value
q-q-plot
updated 3.3 years ago by
Anna
• 0 • written 4.5 years ago by
solanum
• 0
7
votes
2
replies
2.0k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 2.9 years ago by
António Miguel de Jesus Domingues
▴ 510 • written 3.5 years ago by
Alexei Leliavski
▴ 60
4
votes
6
replies
1.4k
views
Question about the usage of Package, qvalue
statistical significance
p-value
q-value
FDR
qvalue
4.4 years ago
manozawa
▴ 10
1
vote
2
replies
920
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
1.2k
views
Dependence of FDR and P-values on sample size
edgeR
FDR
p-value
Benjamini-Hochberg
Differential Analysis
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 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 5.7 years ago by
Michael Love
42k • written 5.7 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
5.8 years ago
modarzi
▴ 10
41
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 7.0 years ago by
yjiangnan
▴ 10
0
votes
0
replies
982
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 6.9 years ago by
Ryan C. Thompson
★ 7.9k • written 6.9 years ago by
ed_isfahani
• 0
2
votes
5
replies
3.2k
views
Limma toptable interpretation check
limma
microarray
fdr
p-value
results
updated 7.0 years ago by
Aaron Lun
★ 28k • written 7.0 years ago by
bhgyu
▴ 30
2
votes
1
reply
2.1k
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
★ 5.2k • 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 3.2 years ago by
Kai_Qi
▴ 20 • written 8.3 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 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
Eleni Christodoulou
▴ 150
5
votes
2
replies
2.4k
views
RankProd: Why are p-values=0?
rankprod
p-value
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 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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Answer: Subsetting RNAseq data | voomaByGroup()
by
Gordon Smyth
50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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