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STATISTICS
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10
votes
14
replies
13k
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how DESeq calculates p-value ?
deseq
differential gene expression
statistics
p-value
updated 3.1 years ago by
Kai_Qi
▴ 20 • written 8.1 years ago by
Giard
▴ 30
25
votes
7
replies
10k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2
rnaseq
statistics
updated 5 months ago by
camillab.
▴ 10 • written 6.5 years ago by
Russ Fraser
▴ 30
19
votes
4
replies
8.0k
views
Confidence intervals on edgeR logFC
edgeR
statistics
confidence interval
updated 8.0 years ago by
nwvidal
• 0 • written 9.5 years ago by
ri.lars
▴ 40
2
votes
2
replies
7.5k
views
edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR
bioconductor
fdr
statistics
differential gene expression
7.3 years ago
jol.espinoz
▴ 40
8
votes
8
replies
6.6k
views
Voom transformation from counts and normalization to negative values
rnaseq
voom
limma
tcga
statistics
updated 5.5 years ago by
Ryan C. Thompson
★ 7.9k • written 5.5 years ago by
Beginner
▴ 60
0
votes
4
replies
5.5k
views
10 multiple comparisons in DESeq2
deseq2
rnaseq
statistics
updated 7.8 years ago by
Michael Love
41k • written 7.8 years ago by
kissmatee
• 0
8
votes
3
replies
3.1k
views
Differing topTable() results with Limma with and without specifying coefficient
limma
microarray
statistics
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
krr
• 0
0
votes
4
replies
2.8k
views
XCMS for targeted metabolomic/lipidomics/proteomics
xcms
metabolomics
lipidomics
statistics
8.2 years ago
Titan
• 0
2
votes
2
replies
2.7k
views
How adjusted p-values are calculated in limma
limma
r
transcriptomics
FDR
statistics
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
Wuschel
▴ 10
1
vote
2
replies
2.7k
views
the statistical test that DESeq2 use
deseq2
statistics
updated 7.1 years ago by
Ryan C. Thompson
★ 7.9k • written 7.1 years ago by
elhamdallalbashi
• 0
1
vote
6
replies
2.6k
views
DESeq2 unbalanced sample size
deseq2
bioconductor
bioinformatics
statistics
updated 13 months ago by
Michael Love
41k • written 5.3 years ago by
casikecola
• 0
3
votes
0
replies
2.1k
views
Job:
Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job
proteomics
Job
statistics
4.4 years ago • updated 4.2 years ago
Gordon Smyth
50k
1
vote
2
replies
2.0k
views
how to perform pre ranked GSEA in R?
r
microarray
statistics
GSEA
updated 7.1 years ago by
predeus
• 0 • written 9.1 years ago by
Nemo
▴ 80
1
vote
0
replies
2.0k
views
Job:
Postdoctoral Research Fellow in Bioinformatics - Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz, Germany
bioinformatician job
rnaseq
statistics
systemsbiology
Job
8.9 years ago
Federico Marini
▴ 150
0
votes
0
replies
1.9k
views
Job:
Full position as Statistician at ETH Zurich in Personalized Medicine Consultancy/Data Analysis
statistics
consultancy
personalized medicine
Job
9.5 years ago
Daniel Stekhoven
▴ 10
0
votes
0
replies
1.8k
views
Job:
Postdoc and PhD student in Bioinformatics/Biostatistics
genomics
NGS
R
genetics
statistics
5.7 years ago • updated 3.3 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.8k
views
News:
Workshop on Statistical Challenges in Single-Cell Biology, April 30 to May 5, 2017, at Villa Monte Verita, Ascona
workshop
statistics
single-cell
News
7.6 years ago
Wolfgang Huber
★ 13k
0
votes
0
replies
1.8k
views
Job:
Bioinformatics Programmer (Statistician) at University of California at San Francisco
R
bioinformatician job
Perl
Python
statistics
Job
7.9 years ago • updated 7.7 years ago
clif.duhn
• 0
1
vote
0
replies
1.8k
views
News:
Workshop Statistical Methods for Post Genomic Data in Munich, February 12-13, 2015
statistics
workshop
news
News
9.5 years ago
gagneur
▴ 10
1
vote
0
replies
1.6k
views
Job:
PhD Positions in Computational Cancer Research
computational biology
image analysis
cancer genomics
statistics
Job
7.3 years ago
Bernd Fischer
▴ 550
0
votes
0
replies
1.5k
views
Job:
Computational Biologist (Genome Statistical Analyst) position in CRUK Manchester Institute, UK
job
bioinformatics
ngs
genomics
statistics
Job
8.1 years ago
Hui Sun Leong
▴ 10
0
votes
0
replies
1.5k
views
Job:
Research Scientist in Biostatistics/Bioinformatics
statistics
genetics
genomics
R
Job
7.1 years ago • updated 7.0 years ago
Luo Weijun
★ 1.6k
2
votes
3
replies
1.5k
views
RNAseq outlier is a critical sample
rnaseq
outlier
statistics
batch effect
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
grastalt27
• 0
0
votes
0
replies
1.5k
views
Job:
Come apply for our Epidemiologist, AncestryHealth role
genomics
genetics
design
statistics
scientist
Job
8.8 years ago
careers
• 0
0
votes
3
replies
1.4k
views
Reading large file (15GB) in R
R
Rstudio
Bioconducter
statistics
updated 2.1 years ago by
Sean Davis
21k • written 2.2 years ago by
Jitendra
▴ 10
3
votes
3
replies
1.4k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2
apeglm
statistics
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
zefrieira
• 0
3
votes
5
replies
1.3k
views
P adjusted values in Deseq2
DESeq2
Statistics
written 3.2 years ago by
Jesus
• 0
0
votes
0
replies
1.3k
views
Job:
Postdoc and PhD student in Bioinformatics/Biostatistics
NGS
R
statistics
genomics
big data
Job
5.1 years ago • updated 4.3 years ago
Luo Weijun
★ 1.6k
0
votes
2
replies
1.2k
views
Compute test-score statistical significance using control-scores from shuffled population
statistics
hypotheses
R
8.0 years ago
Bade
▴ 310
0
votes
0
replies
1.2k
views
Job:
Bioinformaticist, Research Programmer
R
genomics
statistics
Job
7.1 years ago
radel
• 0
0
votes
6
replies
1.2k
views
regression analysis for epic array methylation data using limma
limma
Epigenetics
STATISTICS
R
22 months ago
Jitendra
▴ 10
1
vote
4
replies
1.2k
views
Do the gene set statistics of the ROAST paper correspond to those implemented in the .roastEffects R function?
limma
roast
statistics
source code
gene set testing
5.6 years ago
Andrea Carenzo
• 0
0
votes
0
replies
1.2k
views
Job:
Seeking computational biologists with expertise in RNA-Seq and/or statistics at Immuneering Corporation, Cambridge MA and New York NY
rna-seq
CNS
Neurodegeneration
statistics
computational biology
Job
7.4 years ago
mmartin
▴ 20
0
votes
0
replies
1.2k
views
Job:
Postdoc in Biostatistics/Bioinformatics at UNC Charlotte, NC, USA
genetics/genomics
omics data
statistics
development
R
Job
7.7 years ago • updated 7.5 years ago
Luo Weijun
★ 1.6k
2
votes
4
replies
1.2k
views
Removing batch effect on edgeR when interactons are looked at
rnaseq
edger
statistics
model matrix
updated 6.5 years ago by
Steve Lianoglou
★ 13k • written 6.5 years ago by
David R
▴ 90
1
vote
1
reply
1.2k
views
FPKM t-test vs DEseq2
DESeq2
statistics
rna-seq
updated 11 months ago by
ATpoint
★ 4.0k • written 11 months ago by
SH
• 0
0
votes
0
replies
1.1k
views
DSS DMLTest Prior Estimate of theta dispersion
DSS
dmltest
bayesian
statistics
methylation
6.0 years ago
floriandeckert
▴ 30
0
votes
0
replies
1.1k
views
Two questions about pathifier package
pathways
statistics
microarray
6.2 years ago
arronar
• 0
0
votes
0
replies
1.1k
views
Assigning stats to differential peak locations relative to TSS
chipseeker
chipseq
statistics
6.5 years ago
rbronste
▴ 60
1
vote
0
replies
1.1k
views
Job:
Statistical Research Associate
biostatistics
statistics
sas
git
assay
Job
5.9 years ago
Fred Hutch (Recruiting)
▴ 40
0
votes
5
replies
1.1k
views
Comparing sets of differentially expressed genes
deseq2
rnaseq
statistics
8.5 years ago
sunkid
• 0
0
votes
0
replies
1.1k
views
News:
SCANGEN: Single-cell cancer genomics workshop at ISMB 2018
single cell
cancer genomics
statistics
News
6.0 years ago
kieranrcampbell
▴ 50
0
votes
2
replies
1.1k
views
comparing two GOstats result lists
gostats
statistics
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
sven.schenk
▴ 20
0
votes
0
replies
1.0k
views
Job:
Proteomics Bioinformatician
JobPosting
Proteomics
Statistics
Job
3.3 years ago
Laura
• 0
1
vote
2
replies
1.0k
views
Re-calculation of Padj (P adjusted value)
statistics
Benjamini–Hochberg procedure
deseq2
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
Matan G.
▴ 50
0
votes
2
replies
972
views
News:
Ascona Workshop “Biological systems: from first principles to data-driven modelling and back” 27. 3. - 1. 4. 2022
theory
modeling
statistics
ascona
Workshop
2.4 years ago • updated 14 months ago
Wolfgang Huber
★ 13k
0
votes
0
replies
967
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
4.6 years ago
tatabox
• 0
2
votes
1
reply
964
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 7.8 years ago by
Aaron Lun
★ 28k • written 7.8 years ago by
tati6406
• 0
1
vote
2
replies
930
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays
microarray
probe
statistics
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
ravelarvargas
• 0
0
votes
1
reply
927
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS
GWAS
resampling
resample
statistics
5.1 years ago
naglemi
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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