Showing : limma design matrix • reset
6
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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
7
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8
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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
2
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13
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2.1k
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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
3
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7
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2.3k
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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 Pierre-François Roux • 0
2
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4
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8.3k
views
Limma design and contrast matrix
limma limma design matrix limma contrast matrix
8.1 years ago donny.dw • 0
2
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2
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1.1k
views
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
5
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10
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1.6k
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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
9
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8
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3.1k
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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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2
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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
7
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7
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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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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
11
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9
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1.6k
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Correlation of a Linear Variable
limma limma design matrix
updated 9.1 years ago by 65k • written 9.1 years ago by ▴ 370
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4
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1.3k
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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
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
2
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13
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1.9k
views
problem about (design matrix)
limma limma design matrix design matrix
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
4
votes
3
replies
3.3k
views
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
1
vote
1
reply
840
views
challenging design matrix
limma design matrix differential gene expression limma
updated 7.9 years ago by 50k • written 7.9 years ago by • 0
6
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5
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1.3k
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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
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
1
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2
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1.3k
views
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
2
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1
reply
1.1k
views
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
1
vote
5
replies
1.8k
views
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
3
votes
5
replies
2.1k
views
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
2
votes
8
replies
5.0k
views
limma interaction contrasts
limma contrast matrix limma design matrix limma
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 20
5
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3
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2.1k
views
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
0
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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
3
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2
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8.5k
views
Limma paired sample analysis
limma design matrix limma paired analysis limma
6.6 years ago anandprem1792 ▴ 20
1
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4
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2.7k
views
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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3
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1.0k
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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
2
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2
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939
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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
2
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6
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1.7k
views
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
1
vote
1
reply
838
views
Repeated measurements wtih limma
limma limma design matrix
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 10
3
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2
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1.1k
views
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
5
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9
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1.7k
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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
0
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2
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902
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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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3.9k
views
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
1
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5
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1.7k
views
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
1
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1
reply
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
9
votes
2
replies
5.4k
views
Limma Model Matrix Understanding
limma limma design matrix model matrix
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 370
3
votes
6
replies
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
8
votes
6
replies
1.7k
views
Limma Model Design Question
limma design matrix limma
updated 8.8 years ago by 65k • written 8.8 years ago by ▴ 370
2
votes
1
reply
1.9k
views
design matrix for a 4 groups comparision time series experiment
limma design matrix
updated 8.8 years ago by 65k • written 8.8 years ago by • 0
2
votes
6
replies
1.8k
views
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
1
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5
replies
1.7k
views
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
3
votes
4
replies
1.4k
views
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
6
votes
9
replies
1.5k
views
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
6
votes
3
replies
5.4k
views
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
0
votes
0
replies
923
views
ComBat covariate bias when building centroid based predictors
combat combat sva pamr limma design matrix sva
5.6 years ago jmsendoya • 0
0
votes
0
replies
718
views
Limma making contrasts
limma design matrix design and contrast matrix
6.1 years ago matina • 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…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
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
Comment: Deseq2. decontXcounts not integers. Useful alternative?
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