Showing : paired • reset
7
votes
15
replies
16k
views
DESeq2 paired multifactor test
deseq2 paired
updated 16 months ago by • 0 • written 9.5 years ago by ▴ 20
4
votes
14
replies
5.5k
views
Including technical and biological replicates in Limma block analysis?
limma microarray block paired linear model
9.4 years ago vas ▴ 40
1
vote
9
replies
3.6k
views
LIMMA for paired analysis with adjustment for confounding continuous variables
limma gene expression confounding adjustment paired
8.5 years ago Loodramon • 0
1
vote
6
replies
3.5k
views
Limma: advice needed for best approach for joint paired and unpaired analyses in unbalanced intervention study
limma paired unpaired duplicateCorrelation
updated 9.5 years ago by ▴ 10 • written 9.5 years ago by ★ 3.9k
4
votes
7
replies
3.3k
views
Correct implementation of multifactorial paired analysis in limma software package for DE expression
limma microarray multiple factor design paired
updated 9.2 years ago by 50k • written 9.2 years ago by ▴ 830
3
votes
6
replies
2.7k
views
Limma design/contrast correct?
limma microarray design paired mixed model
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
1
vote
15
replies
2.5k
views
between and within subjects design with batch correction
RNASeqData BatchEffect paired DESeq2
3.1 years ago • updated 3.0 years ago demisa • 0
1
vote
5
replies
2.0k
views
limma paired design matrix 3 factors
limma paired design and contrast matrix
9.5 years ago wim.trypsteen • 0
3
votes
3
replies
1.9k
views
read counts of paired end reads for DESeq2 analysis
deseq featurecounts paired
updated 8.0 years ago by ★ 13k • written 8.0 years ago by • 0
1
vote
5
replies
1.7k
views
diffHic preparePairs() does not identify paired-end reads
diffHic preparePairs paired BAM
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
2
votes
1
reply
1.6k
views
EdgeR: Accounting for batch effects in a pairwise analysis
paired batcheffect
updated 9.3 years ago by 50k • written 9.3 years ago by • 0
6
votes
6
replies
1.6k
views
Limma DEG analysis experiment with partial paired design + batch effect
limma paired batch
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 20
4
votes
9
replies
1.5k
views
limma paired design with continous covariate
limma paired covariate
updated 7.9 years ago by ★ 13k • written 7.9 years ago by ▴ 30
1
vote
2
replies
1.5k
views
Pair-wise Limma Analysis with time series data and two levels (control and treatment)
limma microarray time series DEG paired
updated 4.6 years ago by 50k • written 4.6 years ago by • 0
0
votes
1
reply
1.4k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2 comparison design paired treatment
updated 4.5 years ago by ★ 1.3k • written 4.5 years ago by • 0
2
votes
6
replies
1.4k
views
Nested design matrix in edgeR
edger limma paired blocking ruvseq
updated 4.0 years ago by 50k • written 4.0 years ago by • 0
0
votes
2
replies
1.3k
views
Using merged alignments of PE readlists for DEXSeq
dexseq paired rnaseq samtools merge
updated 8.7 years ago by ★ 1.9k • written 8.7 years ago by • 0
0
votes
1
reply
1.2k
views
WGCNA package with monozygotic twin data
wgcna Twin Analysis within-pair analysis paired
updated 8.9 years ago by ★ 3.0k • written 8.9 years ago by • 0
1
vote
6
replies
1.1k
views
DESeq2 design for paired samples
DESeq2 paired
updated 2.7 years ago by 41k • written 2.7 years ago by ▴ 10
1
vote
3
replies
1.0k
views
How can I run a paired RankProd analysis in R?
RankProd paired RNAseq R
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
0
votes
1
reply
952
views
Subject paired DESeq2 design
DESeq2 paired design
updated 2.7 years ago by 41k • written 2.7 years ago by ▴ 10
3
votes
3
replies
888
views
Paired design in limma
limma paired
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
1
vote
2
replies
769
views
Correct DESeq2 interaction design and results with paired and nested data
deseq2 Paired Nested
updated 4.3 years ago by 41k • written 4.3 years ago by ▴ 10
0
votes
1
reply
649
views
Paired samples in DESeq2
R deseq2 Paired Samples
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
1
vote
1
reply
592
views
DESeq2 paired test (for most samples)
deseq2 paired tumor vs normal
updated 4.1 years ago by 41k • written 4.1 years ago by • 0
0
votes
0
replies
535
views
PROPER for paired samples
PROPER Paired
3.8 years ago christoph8 • 0
0
votes
0
replies
341
views
Csaw - WindowCount : Paired reads unexpectedly filtered out
windowCount csaw paired
10 months ago julie.chevalier • 0
27 results • Page 1 of 1
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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