Showing : Contrasts • reset
3
votes
3
replies
613
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 7 months ago by ★ 4.6k • written 7 months ago by ▴ 10
2
votes
3
replies
614
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 9 months ago by 52k • written 9 months ago by • 0
0
votes
3
replies
1.1k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 17 months ago by 67k • written 17 months ago by • 0
1
vote
2
replies
741
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
18 months ago jovel_juan ▴ 30
3
votes
6
replies
1.4k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.0 years ago mohammedtoufiq91 ▴ 10
1
vote
3
replies
862
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
3
votes
8
replies
4.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.6 years ago by ▴ 10
0
votes
3
replies
1.7k
views
limma voom contrasts
contrasts limma voom
updated 2.8 years ago by 52k • written 2.8 years ago by ▴ 90
0
votes
1
reply
903
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
0
votes
2
replies
1.2k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
3.3 years ago James • 0
0
votes
3
replies
1.3k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.4 years ago by ★ 4.0k • written 3.4 years ago by • 0
2
votes
8
replies
2.5k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.6 years ago Jane ▴ 10
3
votes
8
replies
1.5k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.0 years ago by 67k • written 5.0 years ago by • 0
0
votes
1
reply
1.2k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
0
votes
0
replies
842
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.0 years ago ingerslev • 0
0
votes
1
reply
1.3k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
2
votes
3
replies
1.6k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 180
0
votes
4
replies
1.2k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 5.2 years ago by 52k • written 5.2 years ago by • 0
0
votes
1
reply
830
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 5.6 years ago by 43k • written 5.6 years ago by • 0
3
votes
5
replies
1.7k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 40
2
votes
6
replies
1.3k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 5.8 years ago by 52k • written 5.8 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Awards • All
Popular Question to Ali Barry ▴ 40
Popular Question to gabriel.hoffman ▴ 170
Popular Question to Jenny Drnevich ★ 2.0k
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Locations • All
The city by the bay, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
United Kingdom, 2 hours ago
United States, 3 hours ago
UPF, Barcelona, Spain, 5 hours ago
Traffic: 478 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