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pValue
•
reset
1
vote
12
replies
1.0k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
8 weeks ago
paria.alipour
• 0
0
votes
0
replies
414
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue
logFC
lrtest
MAST
12 months ago
Tadeoye
▴ 20
0
votes
1
reply
1.2k
views
values (NA) in p value Deseq2 (reopen)
pvalue
NA
R
DESeq2
updated 2.4 years ago by
ATpoint
★ 4.0k • written 2.4 years ago by
Johan Largo
• 0
1
vote
2
replies
866
views
How to understand the P-value generated by DEseq2
pValue
updated 3.0 years ago by
Michael Love
41k • written 3.0 years ago by
Kai_Qi
▴ 20
0
votes
6
replies
1.6k
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
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
41k • written 5.1 years ago by
peibo_xu
▴ 10
1
vote
5
replies
2.3k
views
Why the p value and logFC calculated by limma is so small
limma
volcanoplot
pvalue
logFC
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 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 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
ricardo3889
• 0
4
votes
7
replies
2.4k
views
edgeR DEG glmQLFTest
glmQLFTest
pvalue
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
zhang.jianhai
▴ 10
0
votes
3
replies
847
views
p-values smaller than machine epsilon in DESeq2
deseq2
pvalue
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
oscarf
• 0
9
votes
5
replies
4.2k
views
Finding DE genes from RNA-seq data
edgeR
pvalue
qvalue
fpkm
differential gene expression
updated 5.5 years ago by
Steve Lianoglou
★ 13k • written 5.5 years ago by
Harrisonesmith
• 0
4
votes
4
replies
1.7k
views
What doest this p.value distribution mean?
deseq2
pvalue
updated 5.9 years ago by
Michael Love
41k • 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 6.2 years ago by
Michael Love
41k • written 6.2 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 7.1 years ago by
Aaron Lun
★ 28k • written 7.1 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 7.3 years ago by
Koki
▴ 10 • written 7.3 years ago by
hassangiahi
• 0
2
votes
10
replies
8.9k
views
adjusted p-values and p-values problems!
pvalue
adjusted pvalue
r
bonferroni
rna-seq
updated 7.6 years ago by
Michael Love
41k • written 7.6 years ago by
fromhj304
▴ 10
2
votes
4
replies
1.2k
views
ResrtingTools include pvalue NA
reportingtools
deseq2
NA
pvalue
updated 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
NMostajo
▴ 10
0
votes
8
replies
1.6k
views
ReportingTools include pvalue NA and comparissons
R
reportingtools
deseq2
pvalue
coef
updated 7.9 years ago by
Michael Love
41k • 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
5.7k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 17 months ago by
James W. MacDonald
65k • written 8.1 years ago by
serpalma.v
▴ 60
7
votes
11
replies
3.5k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq
dmr
ttest
pvalue
updated 8.2 years ago by
James W. MacDonald
65k • written 8.2 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
65k • written 8.3 years ago by
Sameet Mehta
▴ 30
0
votes
0
replies
1.0k
views
pvalRRHO() does not compute the p-value
RRHO
rank
pvalue
8.6 years ago
aurelien
▴ 10
1
vote
3
replies
1.8k
views
confusing output from EdgeR Glm
edger
logfc
pvalue
updated 8.6 years ago by
Aaron Lun
★ 28k • written 8.6 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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Replies
Comment: Different Shrunk Log2FC according with reference
by
Michael Love
41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
Guangchuang Yu
★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO
by
Guido Hooiveld
★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference
by
andrebolerbarros
▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
ATpoint
★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Votes
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
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