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Showing :
Contrasts
•
reset
3
votes
8
replies
3.3k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
written 24 months ago by
Nicole
▴ 10
2
votes
8
replies
2.0k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
2.9 years ago
Jane
▴ 10
3
votes
5
replies
1.4k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
Pietro
▴ 40
2
votes
3
replies
1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
Keith Hughitt
▴ 180
0
votes
3
replies
1.3k
views
limma voom contrasts
contrasts
limma
voom
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
S T
▴ 90
3
votes
8
replies
1.2k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
s.connell
• 0
2
votes
6
replies
1.1k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
Maiv
• 0
0
votes
1
reply
1.1k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
ananda2
• 0
0
votes
1
reply
1.0k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2
contrasts
reference level
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
ananda2
• 0
0
votes
3
replies
997
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
Mir
• 0
3
votes
6
replies
978
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
0
votes
4
replies
974
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
uridavid.akavia
• 0
0
votes
2
replies
959
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.7 years ago • updated 2.6 years ago
James
• 0
0
votes
1
reply
713
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
Mir
• 0
0
votes
0
replies
674
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
4.4 years ago
ingerslev
• 0
0
votes
1
reply
673
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
kehoe
• 0
1
vote
3
replies
658
views
Limma F-statistic identical for different comparison, why?
limma
F-statistic
contrasts
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
jeltje.van.baren
• 0
0
votes
3
replies
641
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
a26fd14e
• 0
1
vote
2
replies
552
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
10 months ago
jovel_juan
▴ 30
2
votes
3
replies
276
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
JKim
• 0
20 results • Page
1 of 1
Recent ...
Replies
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Answer: get BM error
by
James W. MacDonald
65k
The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…
Answer: How to retrieve gene ontology GO class from gene list?
by
James W. MacDonald
65k
You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…
Comment: Different Shrunk Log2FC according with reference
by
Michael Love
41k
I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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