Showing : limma design matrix • reset
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Different results from limma depending on whether or not I have an intercept term in my model
limma lmfit voom limma design matrix voomwithqualityweights
updated 5.4 years ago by 50k • written 5.4 years ago by ▴ 10
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9
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limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
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ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
5.6 years ago jmsendoya • 0
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Creating a correct limma model with respect to contrast matrix and design matrix
limma limma contrast matrix limma design matrix
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
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Repeated measurements wtih limma
limma limma design matrix
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 10
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6
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1.7k
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Building a biologically meaningful design matrix for limma/voom in a large RNASeq experiment
limma limma-voom limma design matrix confounders
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 10
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Limma making contrasts
limma design matrix design and contrast matrix
6.1 years ago matina • 0
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13
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LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom design matrix limma time-course limma design matrix limma
6.1 years ago SPbeginner • 0
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should subgroups of comparisons be analyzed separately in Limma
limma design matrix
updated 6.4 years ago by ▴ 680 • written 6.4 years ago by ▴ 20
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Design matrix for longitudinal discordant twin analysis with limma
limma limma design matrix limma paired analysis twin analysis
updated 6.4 years ago by ★ 28k • written 6.4 years ago by • 0
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4
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2.7k
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Remove batch effect using individuals as random in the model in Limma
batch effect Coeficents non estimable block random effects limma design matrix
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 10
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Limma paired sample analysis
limma design matrix limma paired analysis limma
6.6 years ago anandprem1792 ▴ 20
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LIMMA 2x2 with time
limma limma design matrix
updated 6.9 years ago by 65k • written 6.9 years ago by ▴ 50
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Correct contrast for testing multi-level interaction effect in limma using combined factors design matrix
limma contrast matrix limma design matrix limma rna-seq limma voom
updated 7.1 years ago by ★ 28k • written 7.1 years ago by • 0
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8
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limma interaction contrasts
limma contrast matrix limma design matrix limma
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
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9
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views
LIMMA paired analysis adjusting for two continuous variables - microarray data
limma limma design matrix limma paired analysis microarray
7.1 years ago danielle.newby • 0
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5
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2.1k
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Limma-voom contrast confusion
limma limma voom limma design matrix limma contrast matrix limma paired analysis
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 10
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5
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1.8k
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Limma: paired multifactor analysis
limma limma design matrix limma contrast matrix limma paired analysis limma-voom
updated 7.2 years ago by 50k • written 7.2 years ago by ▴ 10
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1.1k
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Design matrix for multiple interacting continuous variables in limma
limma limma design matrix
updated 7.5 years ago by 65k • written 7.5 years ago by ▴ 10
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1.6k
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Multi-way interaction design in limma
limma design matrix
7.5 years ago snamjoshi87 ▴ 40
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1.3k
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Limma design matrix for three-treatment crossover study
limma design matrix limma limma contrast matrix crossover study
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 10
7
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4
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3.2k
views
Limma contrast for variables disease, gender and age
limma design matrix limma limma contrast matrix microarrays
7.8 years ago miyuki_iii ▴ 10
6
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5
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1.3k
views
limma & design matrix: for 2-color dyes and 4-comparisons?
limma microarray limma design matrix
updated 7.8 years ago by 50k • written 7.8 years ago by • 0
1
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reply
840
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challenging design matrix
limma design matrix differential gene expression limma
updated 7.9 years ago by 50k • written 7.9 years ago by • 0
4
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3
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3.3k
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limma: model/contrast matrix for 2x3 factorial design
limma multifactorial design design and contrast matrix limma design matrix limma contrast matrix
updated 8.1 years ago by 50k • written 8.1 years ago by • 0
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4
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8.3k
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Limma design and contrast matrix
limma limma design matrix limma contrast matrix
8.1 years ago donny.dw • 0
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1.3k
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Limma --- linear model type I and type III SS problem
limma limma design matrix multiple factor design
updated 8.1 years ago by 50k • written 8.1 years ago by • 0
2
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13
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1.9k
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problem about (design matrix)
limma limma design matrix design matrix
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
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Limma Design Matrix for two channel agilent arrays (direct experimental design)
Limma limma design matrix agilent twochannel
8.3 years ago pm2015 • 0
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5.1k
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Model matrix for anova in limma
limma design matrix microarray limma
updated 8.3 years ago by ★ 13k • written 8.4 years ago by ▴ 60
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7
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2.3k
views
Dealing with missing samples in limma and design matrix questions
limma paired analysis limma design matrix illumina beadchip
8.4 years ago • updated 8.3 years ago clevy ▴ 10
6
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5
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2.1k
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Limma : design and contrast for a timecourse experiment with 2 cell lines
limma limma design matrix timecourse
8.4 years ago • updated 8.3 years ago Pierre-François Roux • 0
2
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2
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1.3k
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limma:question on design for (paired?) 2 dye experiment
limma limma design matrix design and contrast matrix 2-dye
updated 8.5 years ago by 50k • written 8.5 years ago by ★ 3.9k
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4
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limma design matrix question
limma design and contrast matrix limma design matrix
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 30
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3
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Calculating contrasts for continuous variable anad interaction effect in Limma
limma design matrix design and contrast matrix continuous interactions
updated 8.5 years ago by ★ 28k • written 8.5 years ago by ▴ 20
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9
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Help with 2x2 factorial for using LIMMA
limma design matrix limma
updated 8.6 years ago by 65k • written 8.6 years ago by ▴ 50
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4
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1.4k
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Problem regarding the explanation of log-fold changes of individual coefficients in limma after eBayes
limma logfoldchange limma design matrix paired samples affymetrix microarrays
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by ▴ 830
1
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5
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1.7k
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Difference between one-stage and two-stage analyses of multiple microarray experiments in limma
r limma limma design matrix
updated 8.7 years ago by 50k • written 8.7 years ago by • 0
2
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6
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1.8k
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Correct setup of a design matrix for a two-color, interwoven microarray loop design with dye swaps
limma design matrix dye-swap two-colour microarray limma
updated 8.7 years ago by 65k • written 8.7 years ago by • 0
2
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1.9k
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design matrix for a 4 groups comparision time series experiment
limma design matrix
updated 8.7 years ago by 65k • written 8.7 years ago by • 0
8
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6
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Limma Model Design Question
limma design matrix limma
updated 8.8 years ago by 65k • written 8.8 years ago by ▴ 370
3
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6
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1.7k
views
Design that evaluates response to continuous and categorical variables
limma design and contrast matrix design matrix limma design matrix
updated 8.8 years ago by 65k • written 8.8 years ago by ▴ 10
7
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6
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3.9k
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Design and contrast question limma (additive or nested or duplicateCorrelation())??
limma model matrix limma design matrix complex-design
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ★ 3.9k
9
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2
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5.4k
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Limma Model Matrix Understanding
limma limma design matrix model matrix
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 370
9
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8
replies
3.1k
views
LIMMA producing too many significant results
LIMMA limma design matrix affy
updated 9.0 years ago by ★ 13k • written 9.0 years ago by ▴ 30
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1
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7.8k
views
DESeq2: how to construct the design matrix?
deseq2 design matrix limma design matrix
updated 9.0 years ago by 41k • written 9.0 years ago by • 0
1
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5
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1.7k
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limma modeling, paired samples: first disease type disappears from design matrix
limma design matrix limma
updated 9.1 years ago by 50k • written 9.9 years ago by ▴ 90
11
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1.6k
views
Correlation of a Linear Variable
limma limma design matrix
updated 9.1 years ago by 65k • written 9.1 years ago by ▴ 370
1
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1
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1.1k
views
limma: advise needed on (nested?) design + interpretation of coefs
limm multiple factor design limma design matrix
updated 9.3 years ago by 50k • written 9.3 years ago by ★ 3.9k
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2
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1.7k
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difference between two design matrix : how to choose ?
limma design matrix
9.3 years ago kippec • 0
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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…
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Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
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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
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