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p-value
•
reset
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 8.2 years ago by
Giard
▴ 30
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
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
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
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
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
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
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
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 3.4 years ago by
Alexei Leliavski
▴ 60
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
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
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
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
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
0
votes
0
replies
977
views
Question: Enrichment heatmap - GOstats package of R
Gostats
p-value
6.8 years ago
salamandra
▴ 20
0
votes
1
reply
955
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
909
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
0
replies
552
views
DEqMS function "outputResult" reports wrong sca.adj.pval
outputresult
DEqMS
sca.adj.pval
error
p-value
18 months ago
Bastian
• 0
19 results • Page
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Replies
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position)
by
Yveto
• 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap
by
Rory Stark
★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
Michael Love
41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds)
by
HAK
• 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
ATpoint
★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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