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pvalue
•
reset
0
votes
2
replies
294
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
11 weeks ago • updated 10 weeks ago
paul.meraner
• 0
1
vote
12
replies
1.7k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison
DESeq2
InteractionSet
pvalue
10 months ago • updated 9 months ago
paria.alipour
• 0
0
votes
0
replies
711
views
How to extract P-Values and LogFC from lrTest in MAST?
pvalue
logFC
lrtest
MAST
20 months ago
Tadeoye
▴ 20
0
votes
1
reply
1.6k
views
values (NA) in p value Deseq2 (reopen)
pvalue
NA
R
DESeq2
updated 3.1 years ago by
ATpoint
★ 4.6k • written 3.1 years ago by
Johan Largo
• 0
1
vote
2
replies
1.1k
views
How to understand the P-value generated by DEseq2
pValue
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Kai_Qi
▴ 20
0
votes
6
replies
1.9k
views
DEXSeq dispersion outlier
DEXSeq
dispersion
pvalue
5.6 years ago
fiona.dick91
▴ 60
1
vote
6
replies
1.8k
views
Zero pvalues after lfcShrink of DESeq2 package
deseq2
pvalue
lfcshrink
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
peibo_xu
▴ 10
1
vote
5
replies
3.0k
views
Why the p value and logFC calculated by limma is so small
limma
volcanoplot
pvalue
logFC
updated 5.8 years ago by
Gordon Smyth
52k • written 5.8 years ago by
xingxd16
▴ 20
0
votes
9
replies
15k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2
pvalue
visualization
enhancedvolcano
rnaseq
written 5.9 years ago by
ricardo3889
• 0
4
votes
7
replies
2.9k
views
edgeR DEG glmQLFTest
glmQLFTest
pvalue
updated 5.9 years ago by
Gordon Smyth
52k • written 5.9 years ago by
zhang.jianhai
▴ 10
0
votes
3
replies
1.0k
views
p-values smaller than machine epsilon in DESeq2
deseq2
pvalue
updated 6.1 years ago by
Michael Love
43k • written 6.1 years ago by
oscarf
• 0
9
votes
5
replies
5.2k
views
Finding DE genes from RNA-seq data
edgeR
pvalue
qvalue
fpkm
differential gene expression
updated 6.2 years ago by
Steve Lianoglou
★ 13k • written 6.2 years ago by
Harrisonesmith
• 0
4
votes
4
replies
2.0k
views
What doest this p.value distribution mean?
deseq2
pvalue
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
chipolino
• 0
1
vote
1
reply
1.4k
views
fdrtool corrected p-value histograms look weird
pvalue
adjusted pvalue
fdrtool
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
hele7
▴ 20
2
votes
2
replies
2.4k
views
How to control p-value inflation with limma
limma
pvalue
inflation
bacon
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
stephane.cauchi
▴ 10
1
vote
1
reply
3.3k
views
Q value obtained from QValue package is lower than P value?
qvalue
pvalue
r
multiple comparisons
updated 7.9 years ago by
Storey, John D.
▴ 100 • written 7.9 years ago by
tombernardryan
▴ 60
0
votes
1
reply
1.4k
views
meta analysis of clc output(differential expression data )
rnaseq
metaseq
clc output
pvalue
meta analysis
updated 8.0 years ago by
Koki
▴ 10 • written 8.0 years ago by
hassangiahi
• 0
2
votes
10
replies
11k
views
adjusted p-values and p-values problems!
pvalue
adjusted pvalue
r
bonferroni
rna-seq
updated 8.2 years ago by
Michael Love
43k • written 8.2 years ago by
fromhj304
▴ 10
2
votes
4
replies
1.3k
views
ResrtingTools include pvalue NA
reportingtools
deseq2
NA
pvalue
updated 8.5 years ago by
Michael Love
43k • written 8.5 years ago by
NMostajo
▴ 10
0
votes
8
replies
1.9k
views
ReportingTools include pvalue NA and comparissons
R
reportingtools
deseq2
pvalue
coef
updated 8.5 years ago by
Michael Love
43k • written 8.5 years ago by
NMostajo
▴ 10
4
votes
1
reply
2.1k
views
Very low EdgeR Pvalues with very small sample size
edger
pvalue
sample size
updated 8.5 years ago by
Aaron Lun
★ 28k • written 8.5 years ago by
Venu Pullabhatla
▴ 40
6
votes
8
replies
6.6k
views
Does limma calculate pvalues using log2 fold changes or with linear values?
limma
pvalue
log2fc
log2
updated 2.1 years ago by
James W. MacDonald
67k • written 8.7 years ago by
serpalma.v
▴ 60
7
votes
11
replies
4.1k
views
t-statistic cutoff for finding DMRs with bsseq
bsseq
dmr
ttest
pvalue
updated 8.9 years ago by
James W. MacDonald
67k • written 8.9 years ago by
enricoferrero
▴ 660
1
vote
2
replies
1.7k
views
Cannot re-create q-values from the p-values in the DiffTable.
cummeRbund
pvalue
adjusted pvalue
qvalue
updated 8.9 years ago by
James W. MacDonald
67k • written 8.9 years ago by
Sameet Mehta
▴ 30
0
votes
0
replies
1.2k
views
pvalRRHO() does not compute the p-value
RRHO
rank
pvalue
9.3 years ago
aurelien
▴ 10
1
vote
3
replies
2.0k
views
confusing output from EdgeR Glm
edger
logfc
pvalue
updated 9.3 years ago by
Aaron Lun
★ 28k • written 9.3 years ago by
amoltej
▴ 10
4
votes
5
replies
3.1k
views
Is it sensable to use p-value detection in illumina bead array as present, absent or marginal call
illumina
pvalue
updated 9.5 years ago by
svlachavas
▴ 840 • written 9.5 years ago by
Agaz Hussain Wani
▴ 260
27 results • Page
1 of 1
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Replies
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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