Showing : design matrix • reset
18
votes
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
1
vote
18
replies
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
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
11
votes
14
replies
4.3k
views
Setting up the Design Matrix
rnaseq edgeR multiple factor design design matrix
8.3 years ago Yogender Gowtham ▴ 20
2
votes
13
replies
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
2
votes
13
replies
2.1k
views
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
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
3
votes
12
replies
2.8k
views
Questions about complex design in limma regarding an agilent microarray dataset with multiple time points and different biological replicates
limma design matrix multiple time points agilent microarrays
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 80
7
votes
11
replies
3.3k
views
Continuous variable interaction with Groups in design matrix
edger design matrix
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 10
0
votes
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
10
replies
2.1k
views
Design matrix for unbalanced data
edgeR RNA-Seq design matrix multifactorial design
8.2 years ago Yogender Gowtham ▴ 20
2
votes
10
replies
2.8k
views
Time-series analysis with DESeq2
deseq2 time-series design matrix edger
updated 5.2 years ago by 42k • written 5.2 years ago by ★ 1.5k
2
votes
10
replies
1.8k
views
Am I on the right tracks with a 3 factor design in Limma?
r limma design matrix biobase
updated 5.8 years ago by 50k • written 5.8 years ago by • 0
4
votes
9
replies
1.2k
views
Statistical background for computing intial estimates for the means of negative binomially distributed gene counts in DESeq2
deseq2 design matrix
5.3 years ago nikosbosse • 0
0
votes
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
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
3
votes
8
replies
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
1
vote
8
replies
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
2
votes
8
replies
3.7k
views
EdgeR. Analysis with pairing across condition and treatment. Design Matrix
edger ANOVA Design matrix
updated 9.3 years ago by 50k • written 9.3 years ago by • 0
3
votes
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
5
votes
7
replies
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
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
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
0
votes
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
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 8.9 years ago by 65k • written 8.9 years ago by ▴ 10
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
2
votes
6
replies
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
3
votes
6
replies
1.0k
views
Overlapping treatments in the design matrix
edger design matrix
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 10
5
votes
5
replies
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
0
votes
5
replies
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
2
votes
5
replies
3.8k
views
design model matrix for nested factors (edgeR)
edger design matrix model matrix
updated 9.1 years ago by ★ 28k • written 9.1 years ago by • 0
0
votes
5
replies
1.7k
views
DESeq2 package : Error in checkFullRank(modelMatrix) while designing multi factor
DESeq2 multiple factor design design model design matrix rna-seq
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
2
votes
5
replies
847
views
a complicate scenario for Design Matrix
edgeR design matrix
updated 8.0 years ago by ★ 28k • written 8.0 years ago by • 0
1
vote
5
replies
951
views
DESEQ2 design matrix for double knockout interaction with condition
deseq2 model.matrix design matrix
updated 5.0 years ago by 42k • written 5.0 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
4
votes
4
replies
1.7k
views
Is this design matrix correct (treament factor with three levels)?
edger limma design matrix
8.2 years ago Ekarl2 ▴ 80
4
votes
4
replies
1.7k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 6.0 years ago by 50k • written 6.0 years ago by • 0
6
votes
4
replies
2.6k
views
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
4
replies
8.5k
views
Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma differential expression design matrix error eset
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
1
vote
4
replies
825
views
EdgeR multiple factor design question
edger design matrix
7.4 years ago bioinformatics ▴ 10
3
votes
4
replies
4.9k
views
multiple comparison using limma
limma design matrix makecontrasts multiple comparisons
7.3 years ago • updated 7.2 years ago annabelle.congras ▴ 10
1
vote
4
replies
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
votes
4
replies
1.6k
views
edgeR design matrix
edgeR design and contrast matrix design matrix
updated 6.1 years ago by 50k • written 6.2 years ago by ▴ 20
1
vote
4
replies
1.6k
views
edgeR design matrix for 2 variables + batch effect
egdeR design matrix batch effect
updated 4.5 years ago by 50k • written 4.5 years ago by • 0
2
votes
3
replies
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
1
vote
3
replies
927
views
Defining the design matrix
design matrix
7.8 years ago humberto_munoz • 0
0
votes
3
replies
894
views
DESeq2 accounting for two confounders with interaction in the design matrix
deseq2 design matrix multi-confounders linear models rna-seq
updated 4.2 years ago by 42k • written 4.2 years ago by • 0
0
votes
3
replies
1.3k
views
Question on DESeq2 nested model example
deseq2 design matrix
updated 8.5 years ago by 42k • written 8.5 years ago by ★ 3.9k
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
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
50 results • Page 1 of 1
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Replies
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results by ATpoint ★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data by ATpoint ★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
For visualization purposes you can draw an horizontal line at the p-value cutoff that meets the experiment-wide FDR cutoff. For instance, i…
Votes
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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
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