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Showing :
Contrasts
•
reset
3
votes
3
replies
818
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 11 months ago by
ATpoint
★ 4.8k • written 11 months ago by
bioinf
▴ 10
2
votes
3
replies
793
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 12 months ago by
Gordon Smyth
52k • written 12 months ago by
JKim
• 0
0
votes
3
replies
1.3k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
a26fd14e
• 0
1
vote
2
replies
802
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
22 months ago
jovel_juan
▴ 30
3
votes
6
replies
1.6k
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
2.3 years ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
920
views
Limma F-statistic identical for different comparison, why?
limma
F-statistic
contrasts
updated 2.4 years ago by
Gordon Smyth
52k • written 2.4 years ago by
jeltje.van.baren
• 0
3
votes
8
replies
4.8k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
written 2.9 years ago by
Nicole
▴ 10
0
votes
3
replies
1.9k
views
limma voom contrasts
contrasts
limma
voom
updated 3.1 years ago by
Gordon Smyth
52k • written 3.1 years ago by
S T
▴ 90
0
votes
1
reply
965
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
Mir
• 0
0
votes
2
replies
1.2k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
3.6 years ago
James
• 0
0
votes
3
replies
1.4k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 3.7 years ago by
Kevin Blighe
★ 4.0k • written 3.7 years ago by
Mir
• 0
2
votes
8
replies
2.7k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
3.9 years ago
Jane
▴ 10
3
votes
8
replies
1.6k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 5.3 years ago by
James W. MacDonald
68k • written 5.3 years ago by
s.connell
• 0
0
votes
1
reply
1.3k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2
contrasts
reference level
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
ananda2
• 0
0
votes
0
replies
889
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
5.3 years ago
ingerslev
• 0
0
votes
1
reply
1.4k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 5.3 years ago by
Michael Love
43k • written 5.3 years ago by
ananda2
• 0
2
votes
3
replies
1.7k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 5.4 years ago by
Michael Love
43k • written 5.4 years ago by
Keith Hughitt
▴ 180
0
votes
4
replies
1.3k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 5.5 years ago by
Gordon Smyth
52k • written 5.5 years ago by
uridavid.akavia
• 0
0
votes
1
reply
876
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
kehoe
• 0
3
votes
5
replies
1.8k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
Pietro
▴ 40
2
votes
6
replies
1.5k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 6.1 years ago by
Gordon Smyth
52k • written 6.1 years ago by
Maiv
• 0
21 results • Page
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Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Comment: Question on displaying color photo as Greyscale in EBImage
by
Albert
• 0
great and very nice
Comment: European Bioconductor Conference 2023 planning
by
Pandora
• 0
The [Tag Game][1] is not just a simple chase; it involves strategy and tactics as players must think quickly to avoid being tagged. Various…
Votes
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
what the test method for enrichGO in clusterProfiler?
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