Showing : regression • reset
11
votes
3
replies
1.7k
views
Fit a multinomial to RNA-seq count data
voom limma glm multinomial regression
updated 7.7 years ago by ★ 3.2k • written 7.7 years ago by ▴ 110
8
votes
3
replies
6.8k
views
Removing batch effects with sva and combat using the sva package
Regression limma sva Regression limma sva
updated 12.4 years ago by ▴ 60 • written 12.4 years ago by ▴ 650
7
votes
4
replies
4.1k
views
Limma when to use zero intercept
limma regression differential expression linear model
updated 4.2 years ago by 50k • written 4.2 years ago by • 0
6
votes
7
replies
2.1k
views
Multi-level experiment with limma
limma design and contrast matrix differential gene expression regression
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
5
votes
25
replies
795
views
limma models out of memory issue on Slurm HPC
Regression limma STATISITICS HPC
updated 15 days ago by 50k • written 25 days ago by ▴ 10
4
votes
3
replies
983
views
Diffbind for regressing multiple confounding variables (blocking factors)
diffbind block regression deseq2 chipseq
updated 3.5 years ago by ★ 5.1k • written 4.5 years ago by ▴ 10
3
votes
3
replies
1.2k
views
Limma - Two-color group differences *and* correlation with individual differences.
limma regression
updated 7.2 years ago by 50k • written 7.2 years ago by ▴ 30
3
votes
0
replies
2.7k
views
Evidence-based guidelines for use the method="robust" option in lmFit
Microarray Normalization Bayesian Regression Cancer limma Microarray Normalization Cancer
12.9 years ago Richard Friedman ★ 2.0k
2
votes
5
replies
15k
views
Limma design and contrast matrix question.
Microarray Regression limma Microarray Regression limma
updated 10.2 years ago by 65k • written 10.2 years ago by ▴ 350
2
votes
4
replies
1.1k
views
Overfitting in limma
limma Regression overfitting
updated 23 months ago by 50k • written 23 months ago by ▴ 30
2
votes
2
replies
2.2k
views
[limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes
Microarray Regression Microarray Regression
updated 10.4 years ago by 50k • written 10.4 years ago by ▴ 30
2
votes
23
replies
3.5k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 7.6 years ago by 41k • written 7.6 years ago by • 0
1
vote
1
reply
793
views
limma: pvalues for coefficients topTable
TimeSeriesExperiment Regression top limma
updated 2.7 years ago by 65k • written 2.7 years ago by • 0
1
vote
2
replies
3.4k
views
Kernel Ridge Regression in R for Drug-Target Interaction
regression kernel ridge r
updated 7.6 years ago by • 0 • written 8.0 years ago by • 0
1
vote
1
reply
7.1k
views
[LIMMA]lmFit with continuous predictor
Regression limma Regression limma
updated 11.8 years ago by ▴ 130 • written 11.8 years ago by ▴ 210
1
vote
3
replies
2.1k
views
limma report logFC confidence interval?
Regression limma Regression limma
updated 2.8 years ago by 50k • written 13.2 years ago by ▴ 40
1
vote
5
replies
1.8k
views
deseq2 normalized data
regression deseq2 counts
updated 8.6 years ago by 41k • written 8.6 years ago by • 0
1
vote
2
replies
773
views
EdgeR -- differentially expressed genes across a continuous variable
edger continuous regression
updated 5.2 years ago by 65k • written 5.2 years ago by • 0
0
votes
7
replies
1.4k
views
M vs A plot
Microarray Normalization Regression Cancer marray Microarray Normalization Regression
updated 20.2 years ago by ★ 6.0k • written 20.2 years ago by ★ 2.0k
0
votes
1
reply
1.1k
views
question about limma fit differences?
Regression limma Regression limma
updated 20.2 years ago by 50k • written 20.2 years ago by ▴ 20
0
votes
3
replies
1.4k
views
GCRMA: feature request
GO Regression probe gcrma frma GO Regression probe gcrma frma
updated 13.3 years ago by ▴ 250 • written 13.3 years ago by ★ 3.9k
0
votes
1
reply
700
views
mean versus linear model?
Regression limma Regression limma
updated 20.3 years ago by ★ 6.0k • written 20.3 years ago by ▴ 340
0
votes
0
replies
774
views
Re: limma linear model [was: (no subject)]
Regression Regression
19.5 years ago karen ▴ 30
0
votes
0
replies
768
views
limma linear model [was: (no subject)]
Regression Regression
19.5 years ago Gordon Smyth 50k
0
votes
0
replies
984
views
Confusion over limma documentation and design/contrast matrix
GO Regression limma GO Regression limma
19.4 years ago Gordon Smyth 50k
0
votes
0
replies
988
views
Confusion over limma documentation and design/contrast matrix
GO Regression limma GO Regression limma
19.4 years ago michael watson IAH-C ★ 3.4k
0
votes
1
reply
2.1k
views
Dose-Response: Regressiion and ANOVA
Regression DOSE Regression DOSE
updated 19.3 years ago by ▴ 360 • written 19.3 years ago by ▴ 620
0
votes
0
replies
662
views
Gene selection: association with linear response and correction for multi test
Regression limma siggenes Regression limma siggenes
19.1 years ago david neil hayes ▴ 70
0
votes
2
replies
3.5k
views
multtest and Cox regression
Regression multtest Regression multtest
updated 19.0 years ago by ▴ 10 • written 19.0 years ago by ▴ 140
0
votes
0
replies
2.5k
views
Cox MTP question
Microarray Regression multtest Microarray Regression multtest
19.0 years ago kpollard ▴ 110
0
votes
0
replies
1.0k
views
Conference announcement: Compstat 2004
Visualization Bayesian Classification Clustering Regression Visualization Bayesian
20.5 years ago Wolfgang Huber ★ 13k
0
votes
0
replies
1.3k
views
qPCR Event Calendar - winter 2010
SNP qPCR Genetics Normalization Clustering Regression Cancer Breast Xenopus laevis probe
13.4 years ago qPCR Platform - the reference in real-t… ▴ 170
0
votes
5
replies
1.2k
views
limma question: direct two-color design & modeling individual subject effects
SystemsBiology Regression probe limma SystemsBiology Regression probe limma
updated 17.0 years ago by ★ 1.1k • written 17.0 years ago by 50k
0
votes
0
replies
718
views
re: Loess
Regression Regression
19.6 years ago David Lee Duewer ▴ 40
0
votes
0
replies
970
views
Unexpected results using limma with numerical factor - regression intercept?
GO Regression limma convert GO Regression limma convert
19.7 years ago Gordon Smyth 50k
0
votes
0
replies
724
views
Off topic: predoctoral grant
Regression Survival Cancer Regression Survival Cancer
20.6 years ago Ramon Diaz ★ 1.1k
0
votes
0
replies
926
views
RE: Design matrix with multiple genotypes + quantified variables (+cor/regression)
Regression limma Regression limma
19.7 years ago Gordon Smyth 50k
0
votes
0
replies
535
views
Reference on linear models [was LIMMA makeContrasts question]
Regression limma Regression limma
17.4 years ago Gordon Smyth 50k
0
votes
0
replies
867
views
tricky batch problem
Metabolomics Regression Metabolomics Regression
17.4 years ago E. Schwarz ▴ 10
0
votes
0
replies
1.0k
views
Unexpected results using limma with numerical factor - regression intercept?
GO Regression limma GO Regression limma
19.7 years ago Matthew Hannah ▴ 940
0
votes
0
replies
696
views
Reference on linear models
Regression limma Regression limma
17.4 years ago Katherine Lawler ▴ 10
0
votes
0
replies
916
views
Course*** R/S+: Fundamentals and Programming Techniques - Princeton, March 1-2
Microarray Classification Clustering Regression Microarray Classification Clustering
17.2 years ago sue@xlsolutions-corp.com ▴ 570
0
votes
0
replies
725
views
9 Courses: Upcoming July 2007 R/S+ schedule by XLSolutions Corp
Regression Regression
16.9 years ago sue@xlsolutions-corp.com ▴ 570
0
votes
0
replies
714
views
Regressions in multtest
Regression Regression
16.8 years ago Benjamin Otto ▴ 830
0
votes
0
replies
967
views
Pvalue permutation of Linear regression
Regression Regression
16.8 years ago Benjamin Otto ▴ 830
0
votes
1
reply
962
views
batch effects and VSN
Normalization Regression vsn limma oligo Normalization Regression vsn limma oligo
updated 16.6 years ago by ★ 13k • written 16.6 years ago by ▴ 330
0
votes
1
reply
1.3k
views
Bioconductor 2.1 is released
SNP Microarray SAGE Annotation Bayesian Regression GUI CGH hgu95av2 graph Rgraphviz SNP
16.5 years ago Hervé Pagès 16k
0
votes
4
replies
2.1k
views
How to create nested data frames
Regression Regression
16.5 years ago Ana Conesa ▴ 130
0
votes
0
replies
1.2k
views
NEW deadline - Talk & Poster Call - qPCR 2009 Event
SNP qPCR Normalization Visualization Regression Cancer probe microRNA SNP qPCR Cancer
15.3 years ago qPCR Platform - the reference in real-t… ▴ 170
0
votes
0
replies
769
views
p-value adjustment when two or more genes are compared at same time
Regression Cancer multtest Regression Cancer multtest
20.7 years ago Jason Liao ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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