Showing : linear model • reset
4
votes
5
replies
2.9k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 3.7 years ago by 65k • written 3.7 years ago by • 0
7
votes
4
replies
4.2k
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
6
replies
1.2k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 4.2 years ago by ★ 13k • written 4.2 years ago by • 0
0
votes
3
replies
838
views
Problem with including batch effects in linear model in LIMMA- samples are removed
limma batch effects linear model
updated 4.2 years ago by 65k • written 4.2 years ago by ▴ 20
2
votes
1
reply
1.4k
views
Using SVA (surrogate variable analysis) to correct for 'completely' confounded cell type composition in DNA methylation data
sva linear model cell type composition R microarray
4.9 years ago epibio ▴ 10
0
votes
2
replies
968
views
Question re "Group-specific condition effects, individuals nested within groups"
deseq2 linear model
updated 5.5 years ago by 65k • written 5.5 years ago by • 0
2
votes
2
replies
1.4k
views
Building linear model (age effect on gene expression)
bioconductor ALL linear model
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
4
votes
2
replies
1.7k
views
Using limma to model gene expression changes with age
limma linear model
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 20
2
votes
1
reply
993
views
Significant reporter activity with mpralm function
mpra mpralm reporter assay linear model
5.9 years ago ATpoint ★ 4.1k
2
votes
4
replies
4.8k
views
Age covariate continuous vs. categorical
deseq2 linear model covariates age design model
updated 6.3 years ago by 41k • written 6.3 years ago by • 0
3
votes
8
replies
2.0k
views
Differential drug dosage effect between two genotypes in limma
limma dose-response linear model model formula
updated 6.4 years ago by 65k • written 6.4 years ago by ▴ 10
5
votes
2
replies
1.9k
views
DESeq2 batch effect with and without interaction model
deseq2 rna-seq R linear model design matrix
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 10
5
votes
1
reply
1.7k
views
Intercept in design matrix
limma linear model intercept
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
0
votes
1
reply
1.2k
views
Visualizing Linear Model Coefficients in R
R deseq2 graph linear model
updated 6.9 years ago by 41k • written 6.9 years ago by • 0
1
vote
5
replies
2.6k
views
DESeq2: How to find out how well the model fits the data?
rnaseq linear model fit deseq2
updated 7.0 years ago by 41k • written 7.0 years ago by ▴ 10
5
votes
2
replies
2.0k
views
limma for Paired Samples vs. lme
limma linear model paired samples
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
6
votes
7
replies
3.9k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 90
1
vote
2
replies
1.8k
views
edgeR | paired samples | multiple baseline | averaging baseline or not
edger rnaseq baseline linear model negative binomial model
updated 7.9 years ago by 50k • written 8.1 years ago by • 0
1
vote
3
replies
1.5k
views
limma overfitting model due to intercept and yet exclusion of intercept= uninterpretable results
limma microarray linear model statistical modeling model.matrix
8.0 years ago christopher.clarskon15 ▴ 20
2
votes
7
replies
3.1k
views
ballgown custom models
ballgown linear model model matrix custom model
8.1 years ago • updated 8.0 years ago sbcn ▴ 80
0
votes
0
replies
1.1k
views
Inappropriate Statistical Models for Agilent microRNA Microarray Data
agimicrorna linear model
8.1 years ago Dario Strbenac ★ 1.5k
8
votes
8
replies
4.4k
views
Limma: fit a model with duplicateCorrelation()
limma microarray duplicatecorrelation technical replicates linear model
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 150
1
vote
0
replies
1.7k
views
Multiple linear regression model for DMR detection?
methylation linear model dmr bsseq biseq
8.4 years ago enricoferrero ▴ 660
4
votes
9
replies
2.1k
views
How to construct contrasts for a linear model with interactions?
limma contrast linear model
8.5 years ago vedran.franke • 0
5
votes
6
replies
2.3k
views
Translating model formula from DESeq to DEXSeq
dexseq linear model formula
updated 8.5 years ago by ★ 1.9k • written 8.5 years ago by ▴ 110
3
votes
3
replies
2.2k
views
ribosome profiling analysis with different dispersions
deseq2 linear model ribosome profiling stats
updated 8.7 years ago by ★ 7.9k • written 8.7 years ago by ▴ 90
3
votes
6
replies
2.1k
views
Complex Model Design with Bumphunter (Minfi)
minfi bumphunter model.matrix linear model
updated 13 months ago by • 0 • written 8.8 years ago by ▴ 370
2
votes
9
replies
2.0k
views
Check DESeq2 contrasts for exon vs intron changes
deseq2 linear model
updated 8.8 years ago by 41k • written 8.8 years ago by ▴ 90
14
votes
16
replies
2.6k
views
Limma - discrepancy in number of significant genes
limma differential gene expression microarray linear model
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 10
3
votes
6
replies
3.7k
views
Check understanding of linear model
linear model deseq2
updated 9.0 years ago by 65k • written 9.0 years ago by ▴ 90
5
votes
2
replies
3.4k
views
Differences when using voom on a design with or without intercept
limma voom linear model
updated 9.2 years ago by 65k • written 9.2 years ago by ▴ 20
2
votes
3
replies
1.4k
views
Sample power selection for limma analysis in R
limma linear model
updated 9.3 years ago by 50k • written 9.3 years ago by ▴ 830
4
votes
14
replies
5.5k
views
Including technical and biological replicates in Limma block analysis?
limma microarray block paired linear model
9.4 years ago vas ▴ 40
14
votes
19
replies
8.9k
views
DESeq2 Model Design
DESeq2 linear model model
updated 3.0 years ago by 41k • written 9.4 years ago by ▴ 370
3
votes
4
replies
2.7k
views
Help, Statistical test for unbalanced data set
linear model
updated 9.6 years ago by 50k • written 9.6 years ago by ▴ 10
35 results • Page 1 of 1
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Replies
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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