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pValue
•
reset
1
vote
12
replies
1.1k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
3 months ago • updated 11 weeks ago
paria.alipour
• 0
0
votes
0
replies
458
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue
logFC
lrtest
MAST
13 months ago
Tadeoye
▴ 20
0
votes
1
reply
1.2k
views
values (NA) in p value Deseq2 (reopen)
pvalue
NA
R
DESeq2
updated 2.5 years ago by
ATpoint
★ 4.1k • written 2.5 years ago by
Johan Largo
• 0
1
vote
2
replies
885
views
How to understand the P-value generated by DEseq2
pValue
updated 3.1 years ago by
Michael Love
42k • written 3.1 years ago by
Kai_Qi
▴ 20
0
votes
6
replies
1.6k
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
5.1 years ago • updated 5.0 years ago
fiona.dick91
▴ 60
1
vote
6
replies
1.5k
views
Zero pvalues after lfcShrink of DESeq2 package
deseq2
pvalue
lfcshrink
updated 5.1 years ago by
Michael Love
42k • written 5.1 years ago by
peibo_xu
▴ 10
1
vote
5
replies
2.4k
views
Why the p value and logFC calculated by limma is so small
limma
volcanoplot
pvalue
logFC
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
xingxd16
▴ 20
0
votes
8
replies
12k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2
pvalue
visualization
enhancedvolcano
rnaseq
updated 5.3 years ago by
Michael Love
42k • written 5.3 years ago by
ricardo3889
• 0
4
votes
7
replies
2.4k
views
edgeR DEG glmQLFTest
glmQLFTest
pvalue
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
zhang.jianhai
▴ 10
0
votes
3
replies
862
views
p-values smaller than machine epsilon in DESeq2
deseq2
pvalue
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
oscarf
• 0
9
votes
5
replies
4.3k
views
Finding DE genes from RNA-seq data
edgeR
pvalue
qvalue
fpkm
differential gene expression
updated 5.6 years ago by
Steve Lianoglou
★ 13k • written 5.6 years ago by
Harrisonesmith
• 0
4
votes
4
replies
1.8k
views
What doest this p.value distribution mean?
deseq2
pvalue
updated 5.9 years ago by
Michael Love
42k • written 5.9 years ago by
chipolino
• 0
1
vote
1
reply
1.2k
views
fdrtool corrected p-value histograms look weird
pvalue
adjusted pvalue
fdrtool
updated 6.3 years ago by
Michael Love
42k • written 6.3 years ago by
hele7
▴ 20
2
votes
2
replies
2.0k
views
How to control p-value inflation with limma
limma
pvalue
inflation
bacon
updated 7.2 years ago by
Aaron Lun
★ 28k • written 7.2 years ago by
stephane.cauchi
▴ 10
1
vote
1
reply
2.8k
views
Q value obtained from QValue package is lower than P value?
qvalue
pvalue
r
multiple comparisons
updated 7.3 years ago by
Storey, John D.
▴ 100 • written 7.3 years ago by
tombernardryan
▴ 50
0
votes
1
reply
1.2k
views
meta analysis of clc output(differential expression data )
rnaseq
metaseq
clc output
pvalue
meta analysis
updated 7.4 years ago by
Koki
▴ 10 • written 7.4 years ago by
hassangiahi
• 0
2
votes
10
replies
9.0k
views
adjusted p-values and p-values problems!
pvalue
adjusted pvalue
r
bonferroni
rna-seq
updated 7.6 years ago by
Michael Love
42k • written 7.6 years ago by
fromhj304
▴ 10
2
votes
4
replies
1.2k
views
ResrtingTools include pvalue NA
reportingtools
deseq2
NA
pvalue
updated 7.9 years ago by
Michael Love
42k • written 7.9 years ago by
NMostajo
▴ 10
0
votes
8
replies
1.7k
views
ReportingTools include pvalue NA and comparissons
R
reportingtools
deseq2
pvalue
coef
updated 7.9 years ago by
Michael Love
42k • written 7.9 years ago by
NMostajo
▴ 10
4
votes
1
reply
1.8k
views
Very low EdgeR Pvalues with very small sample size
edger
pvalue
sample size
updated 7.9 years ago by
Aaron Lun
★ 28k • written 7.9 years ago by
Venu Pullabhatla
▴ 40
6
votes
8
replies
5.8k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 18 months ago by
James W. MacDonald
66k • written 8.1 years ago by
serpalma.v
▴ 60
7
votes
11
replies
3.6k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq
dmr
ttest
pvalue
updated 8.3 years ago by
James W. MacDonald
66k • written 8.3 years ago by
enricoferrero
▴ 660
1
vote
2
replies
1.4k
views
Cannot re-create q-values from the p-values in the DiffTable.
cummeRbund
pvalue
adjusted pvalue
qvalue
updated 8.3 years ago by
James W. MacDonald
66k • written 8.3 years ago by
Sameet Mehta
▴ 30
0
votes
0
replies
1.1k
views
pvalRRHO() does not compute the p-value
RRHO
rank
pvalue
8.7 years ago
aurelien
▴ 10
1
vote
3
replies
1.8k
views
confusing output from EdgeR Glm
edger
logfc
pvalue
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
amoltej
▴ 10
4
votes
5
replies
2.9k
views
Is it sensable to use p-value detection in illumina bead array as present, absent or marginal call
illumina
pvalue
updated 8.9 years ago by
svlachavas
▴ 830 • written 8.9 years ago by
Agaz Hussain Wani
▴ 260
26 results • Page
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Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq?
by
baptiste.bidon
• 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Comment: ChAMP installation issue
by
Tahirah
• 0
Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
by
James W. MacDonald
66k
Yes, you can use `limma`.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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