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model
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1
vote
3
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899
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baseMean differencies according to the model
Deseq2
model
7.8 years ago
jrivera
• 0
1
vote
7
replies
2.2k
views
Limma linear models
limma
goodness
fit
linear
model
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
nonCodingGene
▴ 10
1
vote
8
replies
1.5k
views
EdgeR model not of full rank
EdgeR
rank
model
6.8 years ago
philip.freda
• 0
0
votes
1
reply
703
views
LRT test in DESeq2 decide on the level of comparisons
DESeq2
LRT
Model
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
JaneDoe
• 0
0
votes
1
reply
3.0k
views
DESeq2 model with blocking factor + interaction term
deseq2
model
updated 8.8 years ago by
Simon Anders
★ 3.7k • written 8.8 years ago by
da.de
▴ 30
5
votes
2
replies
1.8k
views
DESeq2 design matrix for timecourse
deseq2
experimental design
timecourse
rnaseq
model
updated 7.5 years ago by
Michael Love
41k • written 7.5 years ago by
athief
▴ 20
0
votes
2
replies
922
views
Design formula in DESeq2
model
BatchEffect
hidden
Design
DESeq2
2.5 years ago
m.glymenaki
• 0
14
votes
19
replies
8.9k
views
DESeq2 Model Design
DESeq2
linear model
model
updated 3.0 years ago by
Michael Love
41k • written 9.4 years ago by
andrew.j.skelton73
▴ 370
5
votes
5
replies
2.3k
views
edgeR : How to test differential exon expression on case/control study across all time points when accounting for the within subject variability?
egdeR
multiple time points
model.matrix
differential exon usage
model
6.7 years ago
heikki.sarin
▴ 10
4
votes
8
replies
2.1k
views
edgeR: How to set model for glmQLFTest in time-course experiment (compared to glmLRT?
edgeR
edger "glmqlftest()"
timecourse
model
updated 6.7 years ago by
Ryan C. Thompson
★ 7.9k • written 6.7 years ago by
heikki.sarin
▴ 10
3
votes
8
replies
1.9k
views
Differential drug dosage effect between two genotypes in limma
limma
dose-response
linear model
model
formula
updated 6.4 years ago by
James W. MacDonald
65k • written 6.4 years ago by
biominer
▴ 10
0
votes
2
replies
922
views
Diffbind with multiple blocking factors
diffbind
blocking
model
updated 3.5 years ago by
Rory Stark
★ 5.2k • written 4.5 years ago by
melnuesch
▴ 10
1
vote
3
replies
1.0k
views
interaction models DESeq2
deseq2
interaction
model
updated 3.9 years ago by
Michael Love
41k • written 3.9 years ago by
aec
▴ 90
1
vote
1
reply
1.0k
views
DESeq2 Error in checkFullRank(modelMatrix)
DESeq2
ErrorincheckFullRank(modelMatrix)
model
updated 3.4 years ago by
Michael Love
41k • written 3.4 years ago by
Isabelle
• 0
0
votes
1
reply
1.4k
views
Proper dataset form and model for DEXeq analysis
dexseq
rna-seq
model.matrix
model
updated 6.8 years ago by
Michael Love
41k • written 6.8 years ago by
heikki.sarin
▴ 10
0
votes
0
replies
1.2k
views
How construct a model for case-control time-course experiment in DEXseq?
dexseq
timecourse
model.matrix
model
6.7 years ago
heikki.sarin
▴ 10
16 results • Page
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Replies
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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