Showing : contrasts • reset
3
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3
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1.1k
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 17 months ago by ★ 5.0k • written 17 months ago by ▴ 10
2
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3
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1.0k
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 19 months ago by 53k • written 19 months ago by • 0
0
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3
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1.6k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
1
vote
2
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900
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
2.4 years ago jovel_juan ▴ 30
3
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6
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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
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3
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1.1k
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
3
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8
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5.3k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.5 years ago by ▴ 10
0
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3
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2.1k
views
limma voom contrasts
contrasts limma voom
updated 3.6 years ago by 53k • written 3.6 years ago by ▴ 90
0
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1
reply
1.1k
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
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2
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1.4k
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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
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3
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1.6k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 4.2 years ago by ★ 4.0k • written 4.2 years ago by • 0
2
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8
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2.9k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
4.4 years ago Jane ▴ 10
3
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8
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1.9k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
0
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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 43k • written 5.9 years ago by • 0
0
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0
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987
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.9 years ago ingerslev • 0
0
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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 43k • written 5.9 years ago by • 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 43k • written 5.9 years ago by ▴ 180
0
votes
4
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1.5k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 6.1 years ago by 53k • written 6.1 years ago by • 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 43k • written 6.4 years ago by • 0
3
votes
5
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2.0k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 40
2
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6
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1.6k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
21 results • Page 1 of 1
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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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