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P-Value
•
reset
0
votes
0
replies
547
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
954
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
41k • 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 3.2 years ago by
Anna
• 0 • written 4.4 years ago by
solanum
• 0
7
votes
2
replies
2.0k
views
False discovery rates in DEP
p-value
FDR
DEP
updated 2.8 years ago by
António Miguel de Jesus Domingues
▴ 510 • 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
908
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 5.2 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
41k • 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
5.7 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
973
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
3.2k
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
2.1k
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 3.1 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 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
Eleni Christodoulou
▴ 150
5
votes
2
replies
2.3k
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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Recent ...
Replies
Comment: Help with error using camera() in limma
by
Chris
• 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size
by
XW
• 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment
by
XW
• 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
by
James W. MacDonald
65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma
by
James W. MacDonald
65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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