Showing : contrasts • reset
3
votes
3
replies
925
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 12 months ago by ★ 4.8k • written 12 months ago by ▴ 10
2
votes
3
replies
845
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 14 months ago by 52k • written 14 months ago by • 0
0
votes
3
replies
1.3k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 22 months ago by 68k • written 22 months ago by • 0
1
vote
2
replies
818
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
23 months ago jovel_juan ▴ 30
3
votes
6
replies
1.6k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
2.4 years ago mohammedtoufiq91 ▴ 10
1
vote
3
replies
938
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 2.5 years ago by 52k • written 2.5 years ago by • 0
3
votes
8
replies
5.0k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.0 years ago by ▴ 10
0
votes
3
replies
2.0k
views
limma voom contrasts
contrasts limma voom
updated 3.2 years ago by 52k • written 3.2 years ago by ▴ 90
0
votes
1
reply
981
views
DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
2
replies
1.3k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
3.7 years ago James • 0
0
votes
3
replies
1.4k
views
DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
2
votes
8
replies
2.8k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
4.0 years ago Jane ▴ 10
3
votes
8
replies
1.7k
views
Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 5.4 years ago by 68k • written 5.4 years ago by • 0
0
votes
1
reply
1.4k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
0
votes
0
replies
905
views
EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
5.4 years ago ingerslev • 0
0
votes
1
reply
1.4k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 5.4 years ago by 43k • written 5.4 years ago by • 0
2
votes
3
replies
1.7k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 180
0
votes
4
replies
1.3k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 5.6 years ago by 52k • written 5.6 years ago by • 0
0
votes
1
reply
902
views
DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
3
votes
5
replies
1.8k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 40
2
votes
6
replies
1.5k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 6.2 years ago by 52k • written 6.2 years ago by • 0
21 results • Page 1 of 1
Recent ...
Replies
Comment: How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignm by Charles • 0
I am trying this but it is slow. ``` aln2mismatches <- function (gal) { gr <- GRanges(gal) irl <- cigarRangesAlongReferenceSpace(cigar…
Answer: DESeq2 Apeglm Coefficient Reordering / Log2FoldChange Comparison Change by James W. MacDonald 68k
Yes, you can simply flip the sign of the logFC to reverse the direction of the comparison.
Comment: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k
The argument for annotation_col is meant to be a `data.frame`, not a vector. The hint in the error is that it has the wrong number of dimen…
Comment: Heatmap of a transformed deseq object with pheatmap by caroline.zanchi • 0
I used this argument in the second paragraph of code forthe heatmap, this is wehre I got the message Error in `[.default`(annotation_col, c…
Answer: Heatmap of a transformed deseq object with pheatmap by James W. MacDonald 68k
Ah, yes. The non-ASCII character error. My favorite! Please note that `pheatmap` is not a Bioconductor package, so you should be asking …
Votes
Comment: Heatmap of a transformed deseq object with pheatmap
DESeq2: Question about the alpha in summary() and results()
Comment: How to load scRNA-seq data from GEO
limma correction for tumor purity
limma correction for tumor purity
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to gabriella.jacobson-eisenberg ▴ 20
Popular Question to nazaninhoseinkhan • 0
Popular Question to petergrahamclark • 0
Popular Question to atakanekiz ▴ 30
Locations • All
United States, just now
Japan, 1 minute ago
Japan, 2 minutes ago
United States, 6 minutes ago
The city by the bay, 1 hour ago
Traffic: 752 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