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model matrix
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2
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1.4k
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Model matrix for longitudinal pairwise rna-seq data: linear regression or linear mixed model?
limma
model matrix
linear regression
5.6 years ago
agm
• 0
1
vote
2
replies
1.6k
views
DESeq2 design & model matrix not full rank - am I nesting correctly?
deseq2
model matrix
experimental design
multiple factor design
updated 7.0 years ago by
Michael Love
43k • written 7.0 years ago by
amye107
• 0
0
votes
7
replies
1.7k
views
Model matrix not full rank
deseq2
linear combination
model matrix
updated 7.3 years ago by
Michael Love
43k • written 7.3 years ago by
sally_b86
• 0
2
votes
4
replies
1.4k
views
Removing batch effect on edgeR when interactons are looked at
rnaseq
edger
statistics
model matrix
updated 7.3 years ago by
Steve Lianoglou
★ 13k • written 7.3 years ago by
David R
▴ 90
3
votes
6
replies
29k
views
Designing a contrast in DESEQ
deseq2
design and contrast matrix
model matrix
7.9 years ago
mrigaya.mehra
▴ 10
0
votes
8
replies
2.0k
views
DESeq2 glibc error
deseq2
differential gene expression
model matrix
updated 8.0 years ago by
Michael Love
43k • written 8.0 years ago by
gregory.l.stone
▴ 10
4
votes
6
replies
2.8k
views
Find if a covariate has effect on gene expression level using edgeR and DESeq2
edger
deseq2
model matrix
differential expression
8.4 years ago
ta65
• 0
2
votes
7
replies
3.4k
views
ballgown custom models
ballgown
linear model
model matrix
custom model
8.9 years ago • updated 8.8 years ago
sbcn
▴ 80
7
votes
6
replies
4.3k
views
Design and contrast question limma (additive or nested or duplicateCorrelation())??
limma
model matrix
limma design matrix
complex-design
updated 9.6 years ago by
Aaron Lun
★ 28k • written 9.6 years ago by
Guido Hooiveld
★ 4.1k
9
votes
2
replies
5.7k
views
Limma Model Matrix Understanding
limma
limma design matrix
model matrix
updated 9.7 years ago by
Aaron Lun
★ 28k • written 9.7 years ago by
andrew.j.skelton73
▴ 370
2
votes
5
replies
4.3k
views
design model matrix for nested factors (edgeR)
edger
design matrix
model matrix
updated 9.8 years ago by
Aaron Lun
★ 28k • written 9.8 years ago by
silvia.paolucci81
• 0
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Comment: Identifying potentially associated gene set to drug response using GSVA
by
kl2023gege
• 0
Thanks for sharing. You gotta check out Sprunki Phase Games on [Sprunki Phase](https://sprunkiphase.net). It's a wild ride of tunes and tw…
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
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!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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