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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 2.1 years ago by
Nicole
▴ 10
3
votes
8
replies
1.2k
views
Same contrasts returning different edgeR results
edger
limma
contrasts
DGE
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
s.connell
• 0
3
votes
3
replies
275
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 21 days ago by
ATpoint
★ 4.1k • written 21 days ago by
bioinf
▴ 10
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
3
votes
5
replies
1.5k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
Pietro
▴ 40
2
votes
6
replies
1.2k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger
contrasts
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
Maiv
• 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
Michael Love
42k • written 4.5 years ago by
Keith Hughitt
▴ 180
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
2
votes
3
replies
313
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
JKim
• 0
1
vote
2
replies
575
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
11 months ago
jovel_juan
▴ 30
1
vote
3
replies
680
views
Limma F-statistic identical for different comparison, why?
limma
F-statistic
contrasts
updated 18 months ago by
Gordon Smyth
50k • written 18 months ago by
jeltje.van.baren
• 0
0
votes
3
replies
693
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
a26fd14e
• 0
0
votes
3
replies
1.3k
views
limma voom contrasts
contrasts
limma
voom
updated 2.2 years ago by
Gordon Smyth
50k • written 2.2 years ago by
S T
▴ 90
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
Michael Love
42k • written 4.5 years ago by
ananda2
• 0
0
votes
4
replies
1.0k
views
Setting up contrasts with 'limma', patient data, small number of repeats
limma
nanostring
contrasts
updated 4.6 years ago by
Gordon Smyth
50k • written 4.6 years ago by
uridavid.akavia
• 0
0
votes
3
replies
1.0k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
Mir
• 0
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
Michael Love
42k • written 5.0 years ago by
kehoe
• 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
Michael Love
42k • written 4.4 years ago by
ananda2
• 0
0
votes
1
reply
743
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
Mir
• 0
0
votes
0
replies
692
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
4.4 years ago
ingerslev
• 0
0
votes
2
replies
982
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.7 years ago
James
• 0
21 results • Page
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Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat
by
minardsmitha
▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons
by
boczniak767
▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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