Showing : contrasts • reset
2
votes
3
replies
277
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
3
replies
642
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 9 months ago by 65k • written 9 months ago by • 0
1
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2
replies
553
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
10 months ago jovel_juan ▴ 30
3
votes
6
replies
978
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
1
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3
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659
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Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 17 months ago by 50k • written 17 months ago by • 0
3
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8
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3.3k
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 24 months ago by ▴ 10
0
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3
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1.3k
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limma voom contrasts
contrasts limma voom
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 90
0
votes
1
reply
714
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DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
0
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2
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959
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.7 years ago James • 0
0
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3
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998
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
2
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8
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2.0k
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
2.9 years ago Jane ▴ 10
3
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8
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1.2k
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Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 4.4 years ago by 65k • written 4.4 years ago by • 0
0
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1
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1.0k
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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 4.4 years ago by 41k • written 4.4 years ago by • 0
0
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0
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674
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
4.4 years ago ingerslev • 0
0
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1
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1.1k
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DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.4 years ago by 41k • written 4.4 years ago by • 0
2
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3
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1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 180
0
votes
4
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974
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 4.6 years ago by 50k • written 4.6 years ago by • 0
0
votes
1
reply
674
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DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
3
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5
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1.4k
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Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
2
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6
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1.1k
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Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 5.2 years ago by 50k • written 5.2 years ago by • 0
20 results • Page 1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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