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Showing :
contrasts
•
reset
3
votes
3
replies
1.1k
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 17 months ago by
ATpoint
★ 5.0k • written 17 months ago by
bioinf
▴ 10
2
votes
3
replies
1.0k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 19 months ago by
Gordon Smyth
53k • written 19 months ago by
JKim
• 0
0
votes
3
replies
1.6k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
a26fd14e
• 0
1
vote
2
replies
900
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
2.4 years ago
jovel_juan
▴ 30
3
votes
6
replies
1.8k
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
2.9 years ago
mohammedtoufiq91
▴ 10
1
vote
3
replies
1.1k
views
Limma F-statistic identical for different comparison, why?
limma
F-statistic
contrasts
updated 3.0 years ago by
Gordon Smyth
53k • written 3.0 years ago by
jeltje.van.baren
• 0
3
votes
8
replies
5.3k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
written 3.5 years ago by
Nicole
▴ 10
0
votes
3
replies
2.1k
views
limma voom contrasts
contrasts
limma
voom
updated 3.6 years ago by
Gordon Smyth
53k • written 3.6 years ago by
S T
▴ 90
0
votes
1
reply
1.1k
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
Mir
• 0
0
votes
2
replies
1.4k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
4.2 years ago • updated 4.1 years ago
James
• 0
0
votes
3
replies
1.6k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 4.2 years ago by
Kevin Blighe
★ 4.0k • written 4.2 years ago by
Mir
• 0
2
votes
8
replies
2.9k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
4.4 years ago
Jane
▴ 10
3
votes
8
replies
1.9k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 5.8 years ago by
James W. MacDonald
68k • written 5.8 years ago by
s.connell
• 0
0
votes
1
reply
1.4k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2
contrasts
reference level
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
ananda2
• 0
0
votes
0
replies
987
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
5.9 years ago
ingerslev
• 0
0
votes
1
reply
1.5k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
ananda2
• 0
2
votes
3
replies
1.9k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 5.9 years ago by
Michael Love
43k • written 5.9 years ago by
Keith Hughitt
▴ 180
0
votes
4
replies
1.5k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 6.1 years ago by
Gordon Smyth
53k • written 6.1 years ago by
uridavid.akavia
• 0
0
votes
1
reply
982
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 6.4 years ago by
Michael Love
43k • written 6.4 years ago by
kehoe
• 0
3
votes
5
replies
2.0k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 6.6 years ago by
Aaron Lun
★ 29k • written 6.6 years ago by
Pietro
▴ 40
2
votes
6
replies
1.6k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 6.7 years ago by
Gordon Smyth
53k • written 6.7 years ago by
Maiv
• 0
21 results • Page
1 of 1
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Replies
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
James W. MacDonald
68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
Was anyone else able to put the pieces together using the reply above? I read in one 10X sample using DropletUtils::read10xCounts() and thi…
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
dzv20413
• 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments
by
Erik Wright
▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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