Showing : contrasts • reset
3
votes
3
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1.3k
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 21 months ago by ★ 5.0k • written 21 months ago by ▴ 10
2
votes
3
replies
1.2k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 23 months ago by 53k • written 23 months ago by • 0
0
votes
3
replies
1.9k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
1
vote
2
replies
999
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
2.7 years ago jovel_juan ▴ 30
3
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6
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2.0k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
3.2 years ago mohammedtoufiq91 ▴ 10
1
vote
3
replies
1.2k
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
3
votes
8
replies
5.7k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.8 years ago by ▴ 10
0
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3
replies
2.3k
views
limma voom contrasts
contrasts limma voom
updated 4.0 years ago by 53k • written 4.0 years ago by ▴ 90
0
votes
1
reply
1.2k
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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2
replies
1.5k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
4.5 years ago James • 0
0
votes
3
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1.7k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by • 0
2
votes
8
replies
3.2k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
4.7 years ago Jane ▴ 10
3
votes
8
replies
2.0k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
0
votes
1
reply
1.6k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
votes
0
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1.1k
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
6.2 years ago ingerslev • 0
0
votes
1
reply
1.6k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
votes
3
replies
2.0k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 180
0
votes
4
replies
1.7k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 6.4 years ago by 53k • written 6.4 years ago by • 0
0
votes
1
reply
1.1k
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
3
votes
5
replies
2.1k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 6.9 years ago by ★ 29k • written 6.9 years ago by ▴ 40
2
votes
6
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1.8k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 7.0 years ago by 53k • written 7.0 years ago by • 0
21 results • Page 1 of 1
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Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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