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Showing :
contrasts
•
reset
3
votes
8
replies
3.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
written 2.0 years ago by
Nicole
▴ 10
2
votes
8
replies
2.1k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
3.0 years ago • updated 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 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
Keith Hughitt
▴ 180
0
votes
3
replies
1.3k
views
limma voom contrasts
contrasts
limma
voom
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 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
1.0k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
Mir
• 0
3
votes
6
replies
997
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
17 months ago • updated 16 months ago
mohammedtoufiq91
▴ 10
0
votes
4
replies
987
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
970
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.7 years ago
James
• 0
0
votes
1
reply
733
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
Mir
• 0
0
votes
0
replies
682
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
4.4 years ago
ingerslev
• 0
0
votes
1
reply
679
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
667
views
Limma F-statistic identical for different comparison, why?
limma
F-statistic
contrasts
updated 18 months ago by
Gordon Smyth
50k • written 18 months ago by
jeltje.van.baren
• 0
0
votes
3
replies
664
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
a26fd14e
• 0
1
vote
2
replies
565
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
11 months ago
jovel_juan
▴ 30
2
votes
3
replies
295
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
JKim
• 0
3
votes
3
replies
232
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
bioinf
▴ 10
21 results • Page
1 of 1
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Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
gene_bioconductor
▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Answer: How to save the DEXSeq results
by
Michael Love
41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups
by
Robert Castelo
★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways"
by
James W. MacDonald
65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Votes
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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