Showing : Contrasts • reset
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
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
2
votes
8
replies
2.1k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.0 years ago • updated 2.9 years ago Jane ▴ 10
2
votes
6
replies
1.1k
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
998
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
17 months ago mohammedtoufiq91 ▴ 10
3
votes
5
replies
1.4k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
0
votes
4
replies
988
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
3
votes
3
replies
239
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 7 days ago by ★ 4.1k • written 8 days ago by ▴ 10
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
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
1
vote
3
replies
668
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
replies
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
296
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
3
replies
666
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
2
replies
971
views
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
replies
566
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
11 months ago jovel_juan ▴ 30
0
votes
1
reply
735
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
votes
1
reply
680
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 4.9 years ago by 42k • written 4.9 years ago by • 0
0
votes
1
reply
1.0k
views
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
0
votes
1
reply
1.1k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.4 years ago by 42k • written 4.4 years ago by • 0
0
votes
0
replies
684
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: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Awards • All
Popular Question to WouterDeCoster ▴ 130
Scholar to Michael Love 42k
Popular Question to Malcolm Cook ★ 1.6k
Teacher to Gordon Smyth 50k
Popular Question to priyanka.m • 0
Locations • All
Antwerp, Belgium, 3 minutes ago
Belgium, 15 minutes ago
Italy, 22 minutes ago
Singapore, 25 minutes ago
France, 27 minutes ago
Traffic: 705 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6