Showing : design matrix • reset
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1.1k
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DESeq2 accounting for two confounders with interaction in the design matrix
deseq2 design matrix multi-confounders linear models rna-seq
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
votes
2
replies
948
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2 design formula design matrix edgeR ATAC
updated 5.1 years ago by 52k • written 5.1 years ago by • 0
1
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4
replies
2.0k
views
edgeR design matrix for 2 variables + batch effect
egdeR design matrix batch effect
updated 5.2 years ago by 52k • written 5.2 years ago by • 0
0
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2
replies
810
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DESeq2 design matrix choice
deseq2 design matrix
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
2
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1
reply
1.3k
views
Limma Design matrix for time series+treatment+batch effect
limma factorial design matrix microarray
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
1
vote
5
replies
1.2k
views
DESEQ2 design matrix for double knockout interaction with condition
deseq2 model.matrix design matrix
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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1
reply
947
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2 batch sva t-test design matrix
updated 5.7 years ago by 43k • written 5.7 years ago by ▴ 30
0
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0
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878
views
Paired DE analysis in edgeR with trios of samples while blocking for various confounders
edger rnaseq paired analysis design matrix
5.8 years ago svlachavas ▴ 840
2
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10
replies
3.3k
views
Time-series analysis with DESeq2
deseq2 time-series design matrix edger
updated 5.9 years ago by 43k • written 5.9 years ago by ★ 1.5k
0
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1
reply
883
views
differentail expression analysis with interaction terms
edger deseq2 interaction design matrix
updated 6.0 years ago by 67k • written 6.0 years ago by ★ 1.5k
2
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2
replies
1.0k
views
Limma design matrix separate channel analysis with same control
limma design matrix gene expression
updated 6.0 years ago by 52k • written 6.0 years ago by • 0
4
votes
9
replies
1.5k
views
Statistical background for computing intial estimates for the means of negative binomially distributed gene counts in DESeq2
deseq2 design matrix
6.1 years ago nikosbosse • 0
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5
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2.1k
views
DESeq2 package : Error in checkFullRank(modelMatrix) while designing multi factor
DESeq2 multiple factor design design model design matrix rna-seq
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
2
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2
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1.0k
views
DESeq results gives all genes
deseq2 design matrix results
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
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1
reply
1.1k
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 6.2 years ago by 52k • written 6.2 years ago by • 0
2
votes
2
replies
1.5k
views
EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger design matrix glmlrt() glmQFTest() paired design
6.2 years ago oakhamwolf • 0
0
votes
1
reply
1.2k
views
Creating a design matrix
design matrix limma
updated 6.2 years ago by 52k • written 6.4 years ago by ▴ 20
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11
replies
4.2k
views
Limma Design Matrix for Paired Samples with Confouding Factors
limma design matrix paired samples confounding factors
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
5
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7
replies
4.1k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
2
votes
1
reply
797
views
edgeR with related individuals?
edgeR related design matrix
updated 6.3 years ago by 67k • written 6.3 years ago by • 0
5
votes
5
replies
1.8k
views
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix
updated 6.3 years ago by 67k • written 6.3 years ago by ▴ 280
2
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3
replies
1.5k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger design matrix paired samples ruvseq
updated 6.5 years ago by 67k • written 6.5 years ago by • 0
3
votes
8
replies
1.6k
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 6.5 years ago by 52k • written 6.5 years ago by ▴ 110
1
vote
8
replies
2.0k
views
Design matrix for regressing gene expression on a continuous variable - age
limma lmfit design matrix r
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
2
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10
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2.1k
views
Am I on the right tracks with a 3 factor design in Limma?
r limma design matrix biobase
updated 6.6 years ago by 52k • written 6.6 years ago by • 0
0
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1
reply
1.6k
views
Test for differential variability with missMethyl (DiffVar) using block design
missmethyl diffvar design matrix limma block
updated 6.7 years ago by ▴ 50 • written 7.6 years ago by ▴ 190
4
votes
4
replies
2.0k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger differential gene expression model.matrix design matrix
updated 6.7 years ago by 52k • written 6.7 years ago by • 0
3
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7
replies
1.9k
views
single continuous factor
edger design matrix continuous
updated 3.0 years ago by • 0 • written 6.7 years ago by • 0
0
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2
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885
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Limma design matrix
limma design matrix
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 40
0
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1
reply
849
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RNAseq DESeq2 paired data design help
rnaseq design matrix deseq2
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
1
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2
replies
8.6k
views
DESEQ2 design with multiple conditions
deseq2 design matrix
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
0
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2
replies
1.2k
views
DESeq account for using two different siRNA constructs to knockdown same gene
deseq2 design and contrast matrix multiple factor design design matrix
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
3
votes
6
replies
1.5k
views
EdgeR model formula design matrix
edger design matrix paired samples
updated 6.8 years ago by ★ 28k • written 6.8 years ago by • 0
0
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5
replies
1.4k
views
differential expression analysis of cell subtypes mixture
deseq2 edgeR design matrix multifactorial design
updated 6.9 years ago by ★ 28k • written 6.9 years ago by ★ 1.5k
0
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4
replies
2.0k
views
edgeR design matrix
edgeR design and contrast matrix design matrix
updated 6.9 years ago by 52k • written 6.9 years ago by ▴ 20
1
vote
4
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1.1k
views
Deseq multifactor test design full rank error and how to determine one variable only effect.
deseq2 multiple factor design design matrix
6.9 years ago jaime.alvarez.benayas • 0
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13
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2.5k
views
LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom design matrix limma time-course limma design matrix limma
6.9 years ago SPbeginner • 0
1
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18
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2.5k
views
Microarray expression analysis for on factor taking account confounders (covariables)
limma design matrix matrix with covariables
updated 6.9 years ago by ★ 28k • written 6.9 years ago by • 0
5
votes
2
replies
2.2k
views
DESeq2 batch effect with and without interaction model
deseq2 rna-seq R linear model design matrix
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
0
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2
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1.7k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design interactions design matrix deseq2
updated 7.2 years ago by 43k • written 9.2 years ago by ★ 1.5k
3
votes
7
replies
2.4k
views
complex design for chip-seq analysis
chipseq csaw limma design matrix multiple factor design
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ★ 1.5k
6
votes
3
replies
7.3k
views
deseq2 correcting for batch effects
deseq2 batch effect removebatcheffect() design matrix
updated 7.3 years ago by 43k • written 7.3 years ago by ★ 1.5k
1
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2
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1.3k
views
DESeq2 design matrix with a single mock and multiple timepoints
deseq2 design matrix
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
0
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2
replies
3.4k
views
Time-course analysis with limma for >3 time points
limma contrast matrix design matrix multiple time points timecourse
updated 3.7 years ago by • 0 • written 7.6 years ago by ▴ 20
0
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0
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1.3k
views
Possible confounding of variable of interest with batch covariate and Partial NA coefficients when including batch in limma linear model for microarr…
limma batch effect design matrix microarray confounding
7.7 years ago svlachavas ▴ 840
0
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7
replies
2.8k
views
DESeq2: how to identify confounding variable in the design matrix
deseq2 confounders design matrix rnaseq
7.8 years ago lina.faller ▴ 10
3
votes
4
replies
5.6k
views
multiple comparison using limma
limma design matrix makecontrasts multiple comparisons
8.0 years ago annabelle.congras ▴ 10
7
votes
5
replies
1.8k
views
Which is the best design matrix to compare a timecourse between two conditions?
limma voom design matrix timecourse
updated 8.0 years ago by 52k • written 8.0 years ago by ▴ 10
2
votes
6
replies
4.0k
views
RNA-seq paired analysis design
paired samples design matrix limma deseq2 edger
updated 8.0 years ago by 52k • written 8.0 years ago by • 0
0
votes
8
replies
4.6k
views
Design question limma multi variables
limma design matrix
updated 8.0 years ago by ★ 28k • written 8.0 years ago by ▴ 40
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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PDCD1 missing from TxDb.Hsapiens.UCSC.hg38.knownGene?
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Answer: Csaw normalization strategies - general inquiry
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