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
votes
3
replies
1.0k
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 18 months ago by 53k • written 18 months ago by • 0
0
votes
3
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1.5k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.2 years ago by 68k • written 2.3 years ago by • 0
1
vote
2
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889
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
2.3 years ago jovel_juan ▴ 30
3
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6
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1.8k
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.8 years ago mohammedtoufiq91 ▴ 10
1
vote
3
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1.1k
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
3
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8
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5.2k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.4 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
votes
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
4.1 years ago James • 0
0
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3
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1.6k
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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
replies
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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1.8k
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
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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
0
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0
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976
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.8 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
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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
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4
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1.4k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 6.0 years ago by 53k • written 6.0 years ago by • 0
0
votes
1
reply
975
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
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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 6.6 years ago by 53k • written 6.6 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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