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Contrasts
•
reset
2
votes
7
replies
531
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
3 months ago • updated 7 weeks ago
Nicole
• 0
0
votes
3
replies
327
views
limma voom contrasts
contrasts
limma
voom
updated 5 months ago by
Gordon Smyth
46k • written 5 months ago by
S T
▴ 80
0
votes
1
reply
226
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 6 months ago by
Michael Love
37k • written 6 months ago by
Mir
• 0
0
votes
2
replies
395
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
11 months ago
James
• 0
0
votes
3
replies
323
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 12 months ago by
Kevin Blighe
3.6k • written 12 months ago by
Mir
• 0
2
votes
8
replies
714
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
14 months ago
Jane
• 0
3
votes
8
replies
567
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 2.6 years ago by
James W. MacDonald
60k • written 2.6 years ago by
s.connell
• 0
0
votes
1
reply
495
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2
contrasts
reference level
updated 2.7 years ago by
Michael Love
37k • written 2.7 years ago by
ananda2
• 0
0
votes
0
replies
287
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
2.7 years ago
ingerslev
• 0
0
votes
1
reply
632
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2
RNA-Seq
Multifactorial Design
GLM
Contrasts
updated 2.7 years ago by
Michael Love
37k • written 2.7 years ago by
ananda2
• 0
2
votes
3
replies
664
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 2.7 years ago by
Michael Love
37k • written 2.7 years ago by
Keith Hughitt
▴ 170
0
votes
4
replies
470
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 2.9 years ago by
Gordon Smyth
46k • written 2.9 years ago by
uridavid.akavia
• 0
0
votes
1
reply
361
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 3.2 years ago by
Michael Love
37k • written 3.2 years ago by
kehoe
• 0
3
votes
5
replies
741
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 3.4 years ago by
Aaron Lun
★ 27k • written 3.4 years ago by
Pietro
▴ 30
2
votes
6
replies
557
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 3.5 years ago by
Gordon Smyth
46k • written 3.5 years ago by
Maiv
• 0
15 results • Page
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Comment: DESeq2 LFC changes sign after adjusting for surrogates
by
Marie
• 0
Thanks a lot!
Comment: how to use Rsamtools to parse extra fields from STAR alignment
by
Jiping Wang
▴ 90
Thanks so much! That's exactly the solution I am looking for.
Comment: Mapping genome regions to gene symbols
by
michaelwegert
• 0
function > elementLengths() was deprecated in S4Vectors version update 0.16.0 (in 2016?). \ So I used: > elementNROWS() [https://web.m…
Comment: OPLS-DA: confidence interval for accuracy metric
by
etienne.thevenot
▴ 20
- The bootstrapping approach can be used to compute the CIs: see here for an example: Mendez et al. (2019). « A comparative evaluation …
Comment: Data input for aracne2regulon function in viper package
by
xlal
• 0
You are right!And may be we should check the gene symbols cause when I open the expression matrix in EXCEL,it will change some genes into m…
Votes
Comment: DEXSeq: Error in reading counts from htseq "Error in FUN(X[[i]], ...) : subscrip
how to use Rsamtools to parse extra fields from STAR alignment
Comment: how to use Rsamtools to parse extra fields from STAR alignment
Answer: how to use Rsamtools to parse extra fields from STAR alignment
Single Sample GSEA (ssGSEA) and dynamic range of expression
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