Showing : Contrasts • reset
2
votes
8
replies
2.1k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.0 years ago Jane ▴ 10
3
votes
8
replies
3.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.0 years ago by ▴ 10
0
votes
1
reply
685
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
0
votes
4
replies
997
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
2
votes
3
replies
1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.5 years ago by 42k • written 4.5 years ago by ▴ 180
0
votes
1
reply
1.1k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
0
votes
1
reply
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 42k • written 4.4 years ago by • 0
3
votes
8
replies
1.2k
views
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
votes
1
reply
742
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
votes
2
replies
980
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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
1
vote
2
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572
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
11 months ago jovel_juan ▴ 30
0
votes
3
replies
1.3k
views
limma voom contrasts
contrasts limma voom
updated 2.2 years ago by 50k • written 2.2 years ago by ▴ 90
3
votes
3
replies
268
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 18 days ago by ★ 4.1k • written 18 days ago by ▴ 10
3
votes
5
replies
1.5k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 40
2
votes
6
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1.2k
views
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
3
votes
6
replies
1.0k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
17 months ago mohammedtoufiq91 ▴ 10
1
vote
3
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678
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 18 months ago by 50k • written 18 months ago by • 0
0
votes
3
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1.0k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
2
votes
3
replies
310
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
3
replies
688
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 10 months ago by 65k • written 10 months ago by • 0
0
votes
0
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691
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
4.4 years ago ingerslev • 0
21 results • Page 1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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