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Showing :
contrasts
•
reset
3
votes
3
replies
550
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 6 months ago by
ATpoint
★ 4.5k • written 6 months ago by
bioinf
▴ 10
2
votes
3
replies
554
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 7 months ago by
Gordon Smyth
51k • written 7 months ago by
JKim
• 0
0
votes
3
replies
1.1k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 16 months ago by
James W. MacDonald
67k • written 16 months ago by
a26fd14e
• 0
1
vote
2
replies
721
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
17 months ago
jovel_juan
▴ 30
3
votes
6
replies
1.4k
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
23 months ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
841
views
Limma F-statistic identical for different comparison, why?
limma
F-statistic
contrasts
updated 2.0 years ago by
Gordon Smyth
51k • written 2.0 years ago by
jeltje.van.baren
• 0
3
votes
8
replies
4.2k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
written 2.5 years ago by
Nicole
▴ 10
0
votes
3
replies
1.7k
views
limma voom contrasts
contrasts
limma
voom
updated 2.7 years ago by
Gordon Smyth
51k • written 2.7 years ago by
S T
▴ 90
0
votes
1
reply
884
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 2.8 years ago by
Michael Love
42k • written 2.8 years ago by
Mir
• 0
0
votes
2
replies
1.1k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
3.2 years ago
James
• 0
0
votes
3
replies
1.2k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 3.3 years ago by
Kevin Blighe
★ 4.0k • written 3.3 years ago by
Mir
• 0
2
votes
8
replies
2.4k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
3.5 years ago
Jane
▴ 10
3
votes
8
replies
1.5k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 4.9 years ago by
James W. MacDonald
67k • written 4.9 years ago by
s.connell
• 0
0
votes
1
reply
1.2k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2
contrasts
reference level
updated 4.9 years ago by
Michael Love
42k • written 4.9 years ago by
ananda2
• 0
0
votes
0
replies
818
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
4.9 years ago
ingerslev
• 0
0
votes
1
reply
1.3k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
ananda2
• 0
2
votes
3
replies
1.6k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
Keith Hughitt
▴ 180
0
votes
4
replies
1.2k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 5.1 years ago by
Gordon Smyth
51k • written 5.1 years ago by
uridavid.akavia
• 0
0
votes
1
reply
819
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
kehoe
• 0
3
votes
5
replies
1.6k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Pietro
▴ 40
2
votes
6
replies
1.3k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 5.7 years ago by
Gordon Smyth
51k • written 5.7 years ago by
Maiv
• 0
21 results • Page
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Comment: installation error for BiocNeighbors package
by
育
• 0
omitted error2 ~~~ /home/ikutsu/Tsuchiya_NGS/local/include/c++/13.2.0/bits/new_allocator.h: In instantiation of 'void std::__new_allocat…
Comment: installation error for BiocNeighbors package
by
育
• 0
omitted error1 ~~~ /home/ikutsu/Tsuchiya_NGS/local/bin/g++ -std=gnu++17 -fPIC -std=gnu++17 -I"/home/ikutsu/Tsuchiya_NGS/local/lib64/R/i…
Comment: DESeq2 interaction between cancer cells and microenvironment cells
by
monkeymartgameaz
• 0
This is healthy for you. It is your priorities that matter, not those activities you believe you cannot profit from. It is always wise to a…
Answer: Is it possible to parallelise saveHDF5SummarizedExperiment
by
Hervé Pagès
16k
Hi Stefano, Unfortunately HDF5 doesn't support concurrent writing so parallelising is not an option. A few things that maybe could help: …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
It's a simple two-liner in [getsrc.sh][1] ``` awk -F'\t' 'BEGIN {OFS=FS} {if($3 != $11 && $11 != "-") $3 = $11; print $0}' gene_info > tmp…
Votes
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion
A: GOseq analysis with only upregulated or downregulated genes
A: GOseq analysis with only upregulated or downregulated genes
Answer: Properly constructing a hypergeometric test
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