Bioconductor Model matrix

Showing : model matrix • reset

votes

replies

1.6k

views

limma model matrix linear regression

6.6 years ago • updated 6.5 years ago agm • 0

vote

replies

2.0k

views

deseq2 model matrix experimental design multiple factor design

updated 8.0 years ago by Michael Love 43k • written 8.0 years ago by amye107 • 0

votes

replies

2.0k

views

deseq2 linear combination model matrix

updated 8.2 years ago by Michael Love 43k • written 8.2 years ago by sally_b86 • 0

votes

replies

1.7k

views

rnaseq edger statistics model matrix

updated 8.3 years ago by Steve Lianoglou ★ 13k • written 8.3 years ago by David R ▴ 90

votes

replies

31k

views

deseq2 design and contrast matrix model matrix

8.9 years ago mrigaya.mehra ▴ 10

votes

replies

2.4k

views

deseq2 differential gene expression model matrix

updated 8.9 years ago by Michael Love 43k • written 8.9 years ago by gregory.l.stone ▴ 10

votes

replies

3.2k

views

edger deseq2 model matrix differential expression

9.4 years ago ta65 • 0

votes

replies

3.8k

views

ballgown linear model model matrix custom model

9.8 years ago • updated 9.7 years ago sbcn ▴ 80

votes

replies

4.8k

views

limma model matrix limma design matrix complex-design

updated 10.6 years ago by Aaron Lun ★ 29k • written 10.6 years ago by Guido Hooiveld ★ 4.1k

votes

replies

6.1k

views

limma limma design matrix model matrix

updated 10.7 years ago by Aaron Lun ★ 29k • written 10.7 years ago by andrew.j.skelton73 ▴ 370

votes

replies

4.8k

views

edger design matrix model matrix

updated 10.8 years ago by Aaron Lun ★ 29k • written 10.8 years ago by silvia.paolucci81 • 0

11 results • Page 1 of 1

Recent ...

Replies

Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0

Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …

Answer: limpa analysis advice by Gordon Smyth 53k

It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…

Answer: When to use edgeR or limma by Gordon Smyth 53k

The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…

Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k

I updated the above answer today.

Answer: When to use edgeR or limma by James W. MacDonald 68k

I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…

Votes

Answer: When to use edgeR or limma

A: deseq2 - paired samples in 2 sequencing types with very different library sizes

Awards • All