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
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
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
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
6
votes
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
1.0k
views
Overlapping treatments in the design matrix
edger design matrix
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 10
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
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
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
2
votes
1
reply
1.1k
views
Limma Design matrix for time series+treatment+batch effect
limma factorial design matrix microarray
updated 4.8 years ago by ★ 28k • written 4.8 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
2
votes
1
reply
622
views
edgeR with related individuals?
edgeR related design matrix
updated 5.6 years ago by 65k • written 5.6 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
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
2
votes
2
replies
835
views
Limma design matrix separate channel analysis with same control
limma design matrix gene expression
updated 5.3 years ago by 50k • written 5.3 years ago by • 0
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
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
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
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
2
votes
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
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
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
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
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
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
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
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
2
votes
2
replies
2.4k
views
DMRcate cpg.annotate error
dmrcate design matrix
updated 8.5 years ago by ▴ 180 • written 8.5 years ago by ▴ 160
1
vote
1
reply
2.5k
views
EdgeR:Calculating differential expression within/between groups in nested designs
edger nested design matrix differential expression
updated 9.2 years ago by ★ 28k • written 9.2 years ago by • 0
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
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
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
1
vote
4
replies
947
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
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
50 results • Page 1 of 1
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Comment: EGSEA usage with microarray data (with vooma)? by Chris • 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
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.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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