Showing : design matrix • reset
3
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4
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4.9k
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multiple comparison using limma
limma design matrix makecontrasts multiple comparisons
7.3 years ago • updated 7.2 years ago annabelle.congras ▴ 10
5
votes
12
replies
2.0k
views
how to use edgeR analysis RNA-seq data which has four factors
edger design matrix comparing more than two groups multiple factor design
8.3 years ago • updated 8.1 years ago xiaoaozqd • 0
18
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37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
8.9 years ago • updated 8.8 years ago svlachavas ▴ 830
6
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4
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2.6k
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discrepance in DESeq2 results with different design structures
deseq2 differential expression independent filtering pre-filtering design matrix
9.0 years ago Assa Yeroslaviz ★ 1.5k
2
votes
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
6.2 years ago SPbeginner • 0
2
votes
10
replies
2.1k
views
Design matrix for unbalanced data
edgeR RNA-Seq design matrix multifactorial design
8.2 years ago Yogender Gowtham ▴ 20
0
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2
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883
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Anyone see whats causing EdgeR to report Design matrix not of full rank.?
edger design matrix
8.2 years ago nickschurch • 0
1
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18
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2.0k
views
Microarray expression analysis for on factor taking account confounders (covariables)
limma design matrix matrix with covariables
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
2
votes
2
replies
1.3k
views
EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger design matrix glmlrt() glmQFTest() paired design
5.5 years ago oakhamwolf • 0
0
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2
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1.5k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 6.5 years ago by 42k • written 8.5 years ago by ★ 1.5k
3
votes
6
replies
1.3k
views
EdgeR model formula design matrix
edger design matrix paired samples
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
7
votes
5
replies
1.6k
views
Which is the best design matrix to compare a timecourse between two conditions?
limma voom design matrix timecourse
updated 7.3 years ago by 50k • written 7.3 years ago by ▴ 10
0
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2
replies
752
views
Limma design matrix
limma design matrix
updated 6.0 years ago by 50k • written 6.0 years ago by ▴ 40
0
votes
2
replies
774
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Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2 design formula design matrix edgeR ATAC
updated 4.4 years ago by 50k • written 4.4 years ago by • 0
3
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7
replies
1.6k
views
single continuous factor
edger design matrix continuous
updated 2.2 years ago by • 0 • written 6.0 years ago by • 0
4
votes
3
replies
1.3k
views
What is the correct contrast matrix if one treatment must be compared to both of the other two treatments, but separately?
edger limma model.matrix contrast matrix design matrix
updated 7.8 years ago by ▴ 680 • written 7.8 years ago by • 0
4
votes
8
replies
2.5k
views
Can't find any differentially expressed genes
rnaseq differential gene expression design matrix edgeR
updated 9.1 years ago by 50k • written 9.1 years ago by ▴ 10
1
vote
4
replies
825
views
EdgeR multiple factor design question
edger design matrix
7.4 years ago bioinformatics ▴ 10
2
votes
5
replies
847
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a complicate scenario for Design Matrix
edgeR design matrix
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
0
votes
3
replies
698
views
Proper Design Matrix for Paired Samples where endpoint has multiple samples that pair to the same start sample
edger design matrix
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
1
vote
3
replies
927
views
Defining the design matrix
design matrix
7.8 years ago humberto_munoz • 0
2
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1
reply
1.6k
views
using variable in design formula
deseq2 r design matrix
updated 7.7 years ago by 42k • written 7.7 years ago by ▴ 40
4
votes
7
replies
1.1k
views
Design matrix and contrast for RNA knockdown experiment
design matrix limma contrast matrix
updated 7.6 years ago by ★ 28k • written 7.6 years ago by ▴ 180
1
vote
17
replies
1.8k
views
design for edgeR
edger design matrix glmlrt
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
2
votes
2
replies
1.3k
views
DESeq2 multifactorial design with unpaired individuals
deseq2 design matrix
updated 7.3 years ago by 42k • written 7.3 years ago by • 0
0
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8
replies
3.9k
views
Design question limma multi variables
limma design matrix
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 40
2
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6
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3.3k
views
RNA-seq paired analysis design
paired samples design matrix limma deseq2 edger
updated 7.3 years ago by 50k • written 7.3 years ago by • 0
0
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7
replies
2.4k
views
DESeq2: how to identify confounding variable in the design matrix
deseq2 confounders design matrix rnaseq
7.0 years ago lina.faller ▴ 10
0
votes
1
reply
1.3k
views
Test for differential variability with missMethyl (DiffVar) using block design
missmethyl diffvar design matrix limma block
updated 6.0 years ago by ▴ 50 • written 6.9 years ago by ▴ 190
0
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2
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3.0k
views
Time-course analysis with limma for >3 time points
limma contrast matrix design matrix multiple time points timecourse
updated 3.0 years ago by • 0 • written 6.9 years ago by ▴ 20
1
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2
replies
1.1k
views
DESeq2 design matrix with a single mock and multiple timepoints
deseq2 design matrix
updated 6.7 years ago by 42k • written 6.7 years ago by • 0
6
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3
replies
6.9k
views
deseq2 correcting for batch effects
deseq2 batch effect removebatcheffect() design matrix
updated 6.6 years ago by 42k • written 6.6 years ago by ★ 1.5k
3
votes
7
replies
2.0k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ★ 1.5k
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 42k • written 6.5 years ago by ▴ 10
1
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4
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946
views
Deseq multifactor test design full rank error and how to determine one variable only effect.
deseq2 multiple factor design design matrix
6.2 years ago jaime.alvarez.benayas • 0
0
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4
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1.6k
views
edgeR design matrix
edgeR design and contrast matrix design matrix
updated 6.1 years ago by 50k • written 6.1 years ago by ▴ 20
0
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5
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1.1k
views
differential expression analysis of cell subtypes mixture
deseq2 edgeR design matrix multifactorial design
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ★ 1.5k
0
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2
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1.0k
views
DESeq account for using two different siRNA constructs to knockdown same gene
deseq2 design and contrast matrix multiple factor design design matrix
updated 6.1 years ago by 42k • written 6.1 years ago by • 0
0
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1
reply
730
views
RNAseq DESeq2 paired data design help
rnaseq design matrix deseq2
updated 6.0 years ago by 42k • written 6.1 years ago by • 0
1
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2
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7.5k
views
DESEQ2 design with multiple conditions
deseq2 design matrix
updated 6.0 years ago by 42k • written 6.0 years ago by • 0
1
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8
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1.6k
views
Design matrix for regressing gene expression on a continuous variable - age
limma lmfit design matrix r
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
3
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8
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1.3k
views
Design matrix for a two-color experimental design testing for time effect on 3 treated cell-lines, each with its own time=0 control
limma microarray design matrix twochannel
updated 5.8 years ago by 50k • written 5.8 years ago by ▴ 110
2
votes
3
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1.3k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger design matrix paired samples ruvseq
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
0
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1
reply
1.0k
views
Creating a design matrix
design matrix limma
updated 5.5 years ago by 50k • written 5.7 years ago by ▴ 20
5
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5
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1.4k
views
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix
updated 5.6 years ago by 65k • written 5.6 years ago by ▴ 270
2
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1
reply
621
views
edgeR with related individuals?
edgeR related design matrix
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
5
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7
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3.6k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 5.6 years ago by 42k • written 5.6 years ago by ▴ 10
0
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11
replies
3.2k
views
Limma Design Matrix for Paired Samples with Confouding Factors
limma design matrix paired samples confounding factors
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
2
votes
1
reply
913
views
EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
edgeR design matrix contrast
updated 5.5 years ago by 50k • written 5.5 years ago by • 0
2
votes
2
replies
814
views
DESeq results gives all genes
deseq2 design matrix results
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Cannot connect to ExperimentHub server by Jiayu • 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea() by Chris • 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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