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1.1k
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limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 4 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
0
votes
0
replies
191
views
Job:
Statistics Lectureships at St Andrews
JobPosting
computational
statistics
10 weeks ago
Andy Lynch
▴ 120
0
votes
0
replies
234
views
multipollutant models
statistics
Regression
r
limma
5 months ago
Jitendra
▴ 10
0
votes
1
reply
324
views
DEseq2 : Complex design with a mixture of male and female mice
statistics
DESeq2
updated 5 months ago by
Michael Love
41k • written 5 months ago by
lionel.spinelli
• 0
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2
rnaseq
statistics
updated 7 months ago by
camillab.
▴ 10 • written 6.6 years ago by
Russ Fraser
▴ 30
1
vote
1
reply
363
views
Further analysis after limma regression output
statistics
Epigenetics
limma
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
Jitendra
▴ 10
1
vote
1
reply
1.3k
views
FPKM t-test vs DEseq2
DESeq2
statistics
rna-seq
updated 12 months ago by
ATpoint
★ 4.1k • written 12 months ago by
SH
• 0
1
vote
6
replies
2.8k
views
DESeq2 unbalanced sample size
deseq2
bioconductor
bioinformatics
statistics
updated 14 months ago by
Michael Love
41k • written 5.4 years ago by
casikecola
• 0
0
votes
3
replies
950
views
batch effect in EPIC array data
statistics
Epigenetics
R
updated 14 months ago by
Lluís Revilla Sancho
▴ 730 • written 14 months ago by
Jitendra
▴ 10
0
votes
2
replies
1.0k
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
2.5 years ago • updated 15 months ago
Wolfgang Huber
★ 13k
0
votes
0
replies
660
views
Job:
PhD position in Bioinformatics in Jena
Statistics
ComputationalBiology
Aging
MachineLearning
16 months ago
alena.vanboemmel
• 0
0
votes
2
replies
694
views
Results analysis of differential gene expression using DESeq2 package
RnaSeqSampleSize
statistics
DESeq2
updated 16 months ago by
swbarnes2
★ 1.3k • written 17 months ago by
N
• 0
1
vote
0
replies
645
views
Statistical test for genomic annotation by ChIPseeker
statistics
PeakAnnotation
ChIPseeker
GuangchuangYu
21 months ago
arisarkar88
▴ 40
1
vote
0
replies
774
views
Job:
Lecturer in Statistics - School of Mathematics and Statistics - University of St Andrews
computational
teaching
statistics
research
21 months ago
Andy Lynch
▴ 120
1
vote
0
replies
760
views
Job:
Research Fellow in Prostate Cancer Proteomics (Bioinformatics/Stats/Data Analysis) - University of St Andrews
Multiomics
Proteomics
Cancer
Statistics
Bioinformatics
21 months ago
Andy Lynch
▴ 120
0
votes
6
replies
1.3k
views
regression analysis for epic array methylation data using limma
limma
Epigenetics
STATISTICS
R
23 months ago
Jitendra
▴ 10
0
votes
3
replies
1.5k
views
Reading large file (15GB) in R
R
Rstudio
Bioconducter
statistics
updated 2.2 years ago by
Sean Davis
21k • written 2.3 years ago by
Jitendra
▴ 10
3
votes
5
replies
1.4k
views
P adjusted values in Deseq2
DESeq2
Statistics
written 3.3 years ago by
Jesus
• 0
0
votes
0
replies
918
views
Job:
Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
singlecellRNA-Seq
pathview
statistics
R
3.1 years ago • updated 3.0 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
922
views
Job:
Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R
statistics
pathview
singlecellRNA-Seq
3.4 years ago • updated 3.1 years ago
Luo Weijun
★ 1.6k
10
votes
14
replies
13k
views
how DESeq calculates p-value ?
deseq
differential gene expression
statistics
p-value
updated 3.2 years ago by
Kai_Qi
▴ 20 • written 8.2 years ago by
Giard
▴ 30
0
votes
0
replies
941
views
Job:
Bioinformatician at MiroBio, Oxford, UK
Transcriptomics
Bioconductor
Statistics
Job
Biocon
3.2 years ago
m.jackson
• 0
0
votes
0
replies
897
views
Job:
Scientist/Senior Scientist, Statistical Geneticist
Sequencing
Genetics
GeneticsPed
statistics
3.3 years ago
António Miguel de Jesus Domingues
▴ 510
0
votes
0
replies
1.1k
views
Job:
Proteomics Bioinformatician
JobPosting
Proteomics
Statistics
Job
3.4 years ago
Laura
• 0
0
votes
0
replies
1.9k
views
Job:
Postdoc and PhD student in Bioinformatics/Biostatistics
genomics
NGS
R
genetics
statistics
5.8 years ago • updated 3.4 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
764
views
Job:
Two Bioinformatics Fellowship Positions at US EPA
bioinformatics
toxicology
Job
sequenicng
statistics
3.8 years ago • updated 3.5 years ago
whduke
• 0
1
vote
2
replies
1.1k
views
Re-calculation of Padj (P adjusted value)
statistics
Benjamini–Hochberg procedure
deseq2
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
Matan G.
▴ 60
2
votes
0
replies
857
views
Job:
Multiple open positions in biomedical statistics at Eurac Research, Italy
epidemiology
statistics
bioinformatics
Job
3.6 years ago
Johannes Rainer
★ 2.0k
1
vote
0
replies
892
views
Job:
Post-Doctoral Research Fellow, Cancer Genomics
genomics
seattle
bioinformatics
data science
statistics
Job
3.9 years ago
Fred Hutch (Recruiting)
▴ 40
3
votes
0
replies
2.2k
views
Job:
Postdoctoral Scientist, Statistical Bioinformatics and Proteomics, WEHI Australia
job
proteomics
Job
statistics
4.5 years ago • updated 4.3 years ago
Gordon Smyth
50k
0
votes
0
replies
1.3k
views
Job:
Postdoc and PhD student in Bioinformatics/Biostatistics
NGS
R
statistics
genomics
big data
Job
5.2 years ago • updated 4.4 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
784
views
How to handle batch effect and interaction with experimental variables
deseq2
statistics
differential expression
4.5 years ago
A
• 0
0
votes
1
reply
763
views
Exclude interaction terms from the design
deseq2
statistics
modelling
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
polyptwo
• 0
2
votes
2
replies
2.9k
views
How adjusted p-values are calculated in limma
limma
r
transcriptomics
FDR
statistics
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
Wuschel
▴ 10
0
votes
0
replies
1000
views
Proteomics data analysis with DEP no replicates
DEP
Proteomics
Statistics
limma
4.7 years ago
tatabox
• 0
3
votes
3
replies
1.4k
views
Using alternative LFC shrinkage methods for computing p-values in DESeq2
deseq2
apeglm
statistics
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
zefrieira
• 0
0
votes
1
reply
978
views
Efficient resampling in GENESIS or another Bioconductor GWAS package to obtain empirical p-values?
GENESIS
GWAS
resampling
resample
statistics
5.2 years ago
naglemi
▴ 10
0
votes
0
replies
765
views
package for mismatch distribution?
genetics
statistics
5.3 years ago
myriam.croze07
• 0
1
vote
2
replies
939
views
Newbie to all of this
bioconductor
statistics
5.5 years ago
sportwoo
• 0
8
votes
8
replies
6.8k
views
Voom transformation from counts and normalization to negative values
rnaseq
voom
limma
tcga
statistics
updated 5.6 years ago by
Ryan C. Thompson
★ 7.9k • written 5.6 years ago by
Beginner
▴ 60
1
vote
2
replies
964
views
What to do with microarray probes that catch multiple genes?
affymetrix microarrays
microarray
probe
statistics
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
ravelarvargas
• 0
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
5.7 years ago
Andrea Carenzo
• 0
0
votes
2
replies
1.1k
views
comparing two GOstats result lists
gostats
statistics
updated 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
sven.schenk
▴ 20
1
vote
0
replies
1.2k
views
Job:
Statistical Research Associate
biostatistics
statistics
sas
git
assay
Job
6.0 years ago
Fred Hutch (Recruiting)
▴ 40
0
votes
0
replies
1.2k
views
DSS DMLTest Prior Estimate of theta dispersion
DSS
dmltest
bayesian
statistics
methylation
6.1 years ago
floriandeckert
▴ 30
0
votes
0
replies
1.1k
views
News:
SCANGEN: Single-cell cancer genomics workshop at ISMB 2018
single cell
cancer genomics
statistics
News
6.1 years ago
kieranrcampbell
▴ 50
0
votes
0
replies
1.2k
views
Two questions about pathifier package
pathways
statistics
microarray
6.3 years ago
arronar
• 0
2
votes
4
replies
1.2k
views
Removing batch effect on edgeR when interactons are looked at
rnaseq
edger
statistics
model matrix
updated 6.6 years ago by
Steve Lianoglou
★ 13k • written 6.6 years ago by
David R
▴ 90
0
votes
0
replies
1.2k
views
Assigning stats to differential peak locations relative to TSS
chipseeker
chipseq
statistics
6.6 years ago
rbronste
▴ 60
0
votes
0
replies
1.5k
views
Job:
Research Scientist in Biostatistics/Bioinformatics
statistics
genetics
genomics
R
Job
7.2 years ago • updated 7.1 years ago
Luo Weijun
★ 1.6k
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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