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pvalue
•
reset
0
votes
2
replies
616
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
12 months ago
paul.meraner
• 0
1
vote
12
replies
2.5k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
19 months ago
paria.alipour
• 0
0
votes
0
replies
944
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue
logFC
lrtest
MAST
2.5 years ago
Tadeoye
▴ 20
0
votes
1
reply
1.9k
views
values (NA) in p value Deseq2 (reopen)
pvalue
NA
R
DESeq2
updated 3.9 years ago by
ATpoint
★ 5.0k • written 3.9 years ago by
Johan Largo
• 0
1
vote
2
replies
1.2k
views
How to understand the P-value generated by DEseq2
pValue
updated 4.4 years ago by
Michael Love
43k • written 4.5 years ago by
Kai_Qi
▴ 20
0
votes
6
replies
2.2k
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
6.4 years ago
fiona.dick91
▴ 60
1
vote
6
replies
2.2k
views
Zero pvalues after lfcShrink of DESeq2 package
deseq2
pvalue
lfcshrink
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
peibo_xu
▴ 10
1
vote
5
replies
3.7k
views
Why the p value and logFC calculated by limma is so small
limma
volcanoplot
pvalue
logFC
updated 6.6 years ago by
Gordon Smyth
53k • written 6.6 years ago by
xingxd16
▴ 20
0
votes
9
replies
17k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2
pvalue
visualization
enhancedvolcano
rnaseq
written 6.7 years ago by
ricardo3889
• 0
4
votes
7
replies
3.4k
views
edgeR DEG glmQLFTest
glmQLFTest
pvalue
updated 6.7 years ago by
Gordon Smyth
53k • written 6.7 years ago by
zhang.jianhai
▴ 10
0
votes
3
replies
1.2k
views
p-values smaller than machine epsilon in DESeq2
deseq2
pvalue
updated 6.9 years ago by
Michael Love
43k • written 6.9 years ago by
oscarf
• 0
9
votes
5
replies
6.5k
views
Finding DE genes from RNA-seq data
edgeR
pvalue
qvalue
fpkm
differential gene expression
updated 7.0 years ago by
Steve Lianoglou
★ 13k • written 7.0 years ago by
Harrisonesmith
• 0
4
votes
4
replies
2.3k
views
What doest this p.value distribution mean?
deseq2
pvalue
updated 7.3 years ago by
Michael Love
43k • written 7.3 years ago by
chipolino
• 0
1
vote
1
reply
1.6k
views
fdrtool corrected p-value histograms look weird
pvalue
adjusted pvalue
fdrtool
updated 7.6 years ago by
Michael Love
43k • written 7.6 years ago by
hele7
▴ 20
2
votes
2
replies
2.7k
views
How to control p-value inflation with limma
limma
pvalue
inflation
bacon
updated 8.6 years ago by
Aaron Lun
★ 29k • written 8.6 years ago by
stephane.cauchi
▴ 10
1
vote
1
reply
3.8k
views
Q value obtained from QValue package is lower than P value?
qvalue
pvalue
r
multiple comparisons
updated 8.7 years ago by
Storey, John D.
▴ 100 • written 8.7 years ago by
tombernardryan
▴ 60
0
votes
1
reply
1.6k
views
meta analysis of clc output(differential expression data )
rnaseq
metaseq
clc output
pvalue
meta analysis
updated 8.8 years ago by
Koki
▴ 10 • written 8.8 years ago by
hassangiahi
• 0
2
votes
10
replies
13k
views
adjusted p-values and p-values problems!
pvalue
adjusted pvalue
r
bonferroni
rna-seq
updated 9.0 years ago by
Michael Love
43k • written 9.0 years ago by
fromhj304
▴ 10
2
votes
4
replies
1.6k
views
ResrtingTools include pvalue NA
reportingtools
deseq2
NA
pvalue
updated 9.3 years ago by
Michael Love
43k • written 9.3 years ago by
NMostajo
▴ 10
0
votes
8
replies
2.3k
views
ReportingTools include pvalue NA and comparissons
R
reportingtools
deseq2
pvalue
coef
updated 9.3 years ago by
Michael Love
43k • written 9.3 years ago by
NMostajo
▴ 10
4
votes
1
reply
2.5k
views
Very low EdgeR Pvalues with very small sample size
edger
pvalue
sample size
updated 9.3 years ago by
Aaron Lun
★ 29k • written 9.3 years ago by
Venu Pullabhatla
▴ 40
6
votes
8
replies
7.5k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 2.9 years ago by
James W. MacDonald
68k • written 9.5 years ago by
serpalma.v
▴ 60
7
votes
11
replies
4.7k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq
dmr
ttest
pvalue
updated 9.7 years ago by
James W. MacDonald
68k • written 9.7 years ago by
enricoferrero
▴ 680
1
vote
2
replies
1.9k
views
Cannot re-create q-values from the p-values in the DiffTable.
cummeRbund
pvalue
adjusted pvalue
qvalue
updated 9.7 years ago by
James W. MacDonald
68k • written 9.7 years ago by
Sameet Mehta
▴ 30
0
votes
0
replies
1.3k
views
pvalRRHO() does not compute the p-value
RRHO
rank
pvalue
10.1 years ago
aurelien
▴ 10
1
vote
3
replies
2.2k
views
confusing output from EdgeR Glm
edger
logfc
pvalue
updated 10.1 years ago by
Aaron Lun
★ 29k • written 10.1 years ago by
amoltej
▴ 10
4
votes
5
replies
3.4k
views
Is it sensable to use p-value detection in illumina bead array as present, absent or marginal call
illumina
pvalue
updated 10.3 years ago by
svlachavas
▴ 840 • written 10.3 years ago by
Agaz Hussain Wani
▴ 260
27 results • Page
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Comment: Help with defining groups
by
Phinney, Brett
▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness
by
massimo
• 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package
by
ksankaran
• 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
ATpoint
★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
ATpoint
★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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