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
830
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
964
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 5.8 years ago by 50k • written 5.8 years ago by ▴ 20
2
votes
1
reply
990
views
Significant reporter activity with mpralm function
mpra mpralm reporter assay linear model
5.9 years ago ATpoint ★ 4.0k
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
1.9k
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 6.4 years ago by 41k • written 6.4 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 6.9 years ago by 41k • written 6.9 years ago by ▴ 10
5
votes
2
replies
2.0k
views
limma for Paired Samples vs. lme
limma linear model paired samples
updated 6.9 years ago by ★ 28k • written 6.9 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 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 90
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
7.9 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
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
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
8.4 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 8.8 years ago by 65k • written 8.8 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
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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Popular Question to Leo Lahti ▴ 40
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