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Showing :
contrasts
•
reset
3
votes
8
replies
3.3k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression
contrasts
interaction
DESeq2
written 24 months ago by
Nicole
▴ 10
2
votes
8
replies
2.0k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression
DESeq2
contrasts
2.9 years ago
Jane
▴ 10
3
votes
5
replies
1.4k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
Pietro
▴ 40
2
votes
3
replies
1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
Keith Hughitt
▴ 180
0
votes
3
replies
1.3k
views
limma voom contrasts
contrasts
limma
voom
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
S T
▴ 90
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
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
Gordon Smyth
50k • written 5.2 years ago by
Maiv
• 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
Michael Love
41k • written 4.4 years ago by
ananda2
• 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
41k • written 4.4 years ago by
ananda2
• 0
0
votes
3
replies
1.0k
views
DESeq2: difficulty with contrasts and main effects
DESeq2
phyloseq
contrasts
updated 2.7 years ago by
Kevin Blighe
★ 3.9k • written 2.7 years ago by
Mir
• 0
3
votes
6
replies
979
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
0
votes
4
replies
977
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
2
replies
961
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable
voom
contrasts
2.7 years ago
James
• 0
0
votes
1
reply
717
views
DESeq2 2x3 design contrast question
DESeq2
contrasts
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
Mir
• 0
0
votes
1
reply
675
views
DESeq2 compairson of 3 samples from 1 type
deseq2
multiple factor design
contrasts
experimental design
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
kehoe
• 0
0
votes
0
replies
675
views
EdgeR: Transforming coefficients before testing for differential expression
edger
contrasts
model.matrix
circadian
4.4 years ago
ingerslev
• 0
1
vote
3
replies
660
views
Limma F-statistic identical for different comparison, why?
limma
F-statistic
contrasts
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
jeltje.van.baren
• 0
0
votes
3
replies
647
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison
DESeq2
Genetics
contrasts
RNASeq
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
a26fd14e
• 0
1
vote
2
replies
555
views
Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts
DESeq2
10 months ago
jovel_juan
▴ 30
2
votes
3
replies
280
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
JKim
• 0
20 results • Page
1 of 1
Recent ...
Replies
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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