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Contrast
•
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0
votes
3
replies
269
views
I have a problem when I run DESeq2 with one variable with 8 levels, I can't find the contrast for any comparison with level 8
Contrast
factors
levels
3 months ago
Edgar
• 0
0
votes
1
reply
351
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast
design
DESeq2
continuous
updated 14 months ago by
Michael Love
39k • written 14 months ago by
tiansy
• 0
2
votes
3
replies
646
views
Contrast treated samples against both scramble and untreated controls
design
contrast
DESeq2
updated 15 months ago by
Michael Love
39k • written 15 months ago by
oliver.ziff
• 0
0
votes
1
reply
410
views
Interaction using a single factor model DESeq2
synergy
DESeq2
RNA-seq
contrast
18 months ago
slcno
• 0
2
votes
9
replies
3.4k
views
Contrasts in DESeq2
deseq2
contrast
updated 6 months ago by
梓琪
• 0 • written 2.3 years ago by
bahmanik@msu.edu
▴ 30
3
votes
2
replies
434
views
LIMMA Time descendant design
limma
time-dependant
contrast
updated 2.4 years ago by
James W. MacDonald
62k • written 2.4 years ago by
anoopta88
▴ 10
5
votes
10
replies
744
views
Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2
DGE
contrast
updated 2.6 years ago by
Michael Love
39k • written 2.6 years ago by
llooll1
• 0
1
vote
1
reply
20k
views
lfcShrink doesn't work with contrasts
lfcShrink
contrast
design
deseq2
updated 3.1 years ago by
Michael Love
39k • written 3.1 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
402
views
same results changing contrast function
deseq2
contrast
DEG
updated 3.2 years ago by
Michael Love
39k • written 3.2 years ago by
ire.ontiveros
• 0
0
votes
4
replies
1.2k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2
contrast
design
3.3 years ago
luciest.rodriguez
• 0
1
vote
3
replies
2.4k
views
Multi-factor analysis Deseq2
deseq2
contrast
LTR
4.3 years ago • updated 3.4 years ago
Iryna
• 0
1
vote
5
replies
620
views
dseq2 results synergy contrast
deseq2
contrast
synergy
updated 3.7 years ago by
Michael Love
39k • written 3.7 years ago by
steven wink
▴ 90
0
votes
9
replies
1.1k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
4.0 years ago
ariel
▴ 10
6
votes
7
replies
1.0k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2
contrast
ratio of ratio
updated 4.0 years ago by
Michael Love
39k • written 4.0 years ago by
Fischer-philipp
▴ 30
3
votes
5
replies
933
views
lfcShrink, interactions, and ashr
deseq2
lfcshrink
contrast
updated 4.2 years ago by
Michael Love
39k • written 4.2 years ago by
jurbach
▴ 10
2
votes
1
reply
515
views
EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
edgeR
design matrix
contrast
updated 4.2 years ago by
Gordon Smyth
47k • written 4.2 years ago by
sdalin
• 0
0
votes
5
replies
874
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2
rna-seq
interactions
contrast
updated 4.4 years ago by
Michael Love
39k • written 4.4 years ago by
Maithê Barros
▴ 10
0
votes
3
replies
640
views
A contrast with four simultaneous conditions for DESeq2?
DESeq2
contrast
results
updated 4.6 years ago by
Michael Love
39k • written 4.6 years ago by
jan.soderman
• 0
1
vote
5
replies
1.7k
views
DESeq2 Subsetting gives error in contrasts - can be applied only to factors with 2 or more levels
deseq2
multiple factor design
contrast
4.6 years ago
russell.stewart.j
• 0
3
votes
4
replies
6.2k
views
edgeR design matrix and contrasts: how to make contrast between groups that aren't shown in the design matrix columns?
edger
design and contrast matrix
contrast
limma contrast matrix
limma
updated 5.0 years ago by
Gordon Smyth
47k • written 5.0 years ago by
cafelumiere12
▴ 20
9
votes
1
reply
2.7k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2
model.matrix
GLM
contrast
updated 5.1 years ago by
Michael Love
39k • written 5.1 years ago by
serpalma.v
▴ 60
2
votes
4
replies
924
views
Multiple test corrections for planed contrasts
deseq2
multiple comparisons
contrast
updated 5.2 years ago by
James W. MacDonald
62k • written 5.2 years ago by
serpalma.v
▴ 60
0
votes
4
replies
1.3k
views
Time points and donors - errors with contrasts
deseq2
contrast
updated 5.2 years ago by
Michael Love
39k • written 5.6 years ago by
sasha
• 0
0
votes
2
replies
711
views
Discrepancy in extracting contrasts
deseq2
resultsnames
batch effect
contrast
updated 5.3 years ago by
Michael Love
39k • written 5.3 years ago by
pkachroo
▴ 10
2
votes
5
replies
1.8k
views
Why does limma contrast.fit produces NA's for all contrast although missing data only in one condition?
limma
contrast
missing data
lmfit
makecontrasts
updated 5.4 years ago by
Gordon Smyth
47k • written 5.5 years ago by
wewolski
▴ 10
0
votes
2
replies
1.2k
views
DESEq2 contrast statement syntax and design statement question
deseq2
interactions
contrast
updated 5.5 years ago by
Michael Love
39k • written 5.5 years ago by
grashow
▴ 10
16
votes
7
replies
10.0k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2
lfc
coef
contrast
updated 5.5 years ago by
Michael Love
39k • written 5.5 years ago by
Anke Busch
▴ 10
2
votes
2
replies
1.7k
views
EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR
ANOVA
t-test
contrast
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
Maiv
• 0
2
votes
5
replies
3.8k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2
results
contrast
padj
updated 5.7 years ago by
Michael Love
39k • written 5.7 years ago by
courtney.stairs
• 0
0
votes
1
reply
1.1k
views
how to extract complex contrast with DESeq2
contrast
DESeq2
differential gene expression
updated 5.8 years ago by
Michael Love
39k • written 5.8 years ago by
aec
▴ 90
0
votes
7
replies
2.9k
views
Computing contrasts with a covariate using edgeR glmLRT()
edger
contrast
covariate
glmlrt()
5.8 years ago
Jeff Skinner
• 0
3
votes
19
replies
2.6k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma
batch effect
covariates
contrast
differential gene expression
5.9 years ago
mheydarpour
▴ 10
0
votes
1
reply
1.2k
views
intra-sample time series comparison using DESeq2
deseq2
time course
rnaseq
design
contrast
updated 5.9 years ago by
Michael Love
39k • written 5.9 years ago by
prppmet
• 0
2
votes
13
replies
3.4k
views
DESeq2 log fold change estimates for factors with many levels
deseq2
lfce
contrast
6.0 years ago
crfitzpat
• 0
2
votes
3
replies
868
views
Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2
contrast
updated 6.0 years ago by
Michael Love
39k • written 6.0 years ago by
sebastiano.curreli
• 0
0
votes
2
replies
771
views
edgeR constrast drug treatments and time points
edgeR
contrast
updated 6.3 years ago by
Aaron Lun
★ 28k • written 6.3 years ago by
sergio.martinezcuesta
▴ 10
0
votes
3
replies
1.4k
views
limma camera function Multiple contrasts
limma
microarray
contrast
camera
updated 6.4 years ago by
Gordon Smyth
47k • written 6.4 years ago by
gaby8638
▴ 20
2
votes
6
replies
977
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de
contrast
design and contrast matrix
updated 6.7 years ago by
Aaron Lun
★ 28k • written 6.7 years ago by
nooshin
▴ 300
1
vote
6
replies
814
views
Are these contrasts correct for use in DESeq2?
deseq2
contrast
updated 6.7 years ago by
Michael Love
39k • written 6.7 years ago by
Jane Merlevede
▴ 90
2
votes
2
replies
1.6k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2
rnaseq
contrast
multiple comparisons
fdrtool
6.7 years ago
sebastiano.curreli
• 0
2
votes
6
replies
1.4k
views
Seeking confirmation on manually setting contrasts for a 3-factor design in DESeq2 with multiple interaction terms
deseq2
multiple factor design
interactions
design and contrast matrix
contrast
updated 6.8 years ago by
Michael Love
39k • written 6.8 years ago by
piensaglobalmente
▴ 10
2
votes
4
replies
4.4k
views
Interaction terms in DESeq2 contrasts
deseq2
interactions
design and contrast matrix
contrast
6.8 years ago
dwzhang.wisc
▴ 20
2
votes
5
replies
4.6k
views
DESeq2 multifactor experiment design
deseq2
LRT
multifactor
contrast
interactions
7.0 years ago
rclaire
▴ 20
6
votes
1
reply
2.0k
views
DESeq2, difficulties with multi-factor design
DESeq2
multiple factor design
experimental design
contrast
updated 7.2 years ago by
Michael Love
39k • written 7.2 years ago by
anton.kratz
▴ 60
4
votes
9
replies
1.4k
views
How to construct contrasts for a linear model with interactions?
limma
contrast
linear model
7.2 years ago
vedran.franke
• 0
1
vote
4
replies
995
views
Specificity of gene expression
differential gene expression
specific expression
contrast
deseq2
7.3 years ago
arrigonialberto86
• 0
0
votes
1
reply
1.3k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2
design and contrast matrix
interactions
contrast
updated 7.3 years ago by
Michael Love
39k • written 7.3 years ago by
moldach
▴ 20
3
votes
5
replies
1.1k
views
pass limma contrast matrix variable
contrast
limma
updated 7.4 years ago by
Gordon Smyth
47k • written 7.4 years ago by
John linux-user
▴ 210
6
votes
2
replies
4.1k
views
All same padj of contrast results in the DESeq2
deseq2
padj
contrast
results
updated 7.5 years ago by
Michael Love
39k • written 7.5 years ago by
jjinhyoungkim
▴ 20
7
votes
9
replies
3.4k
views
DESeq2: Compare expression of one group to the mean of others
deseq2
heterosis
contrast
design and contrast matrix
updated 7.6 years ago by
Michael Love
39k • written 7.6 years ago by
johntlovell
▴ 10
50 results • Page
1 of 1
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Comment: DESeq2 and heatmap for multiple comparisons
by
artem.vorobyev
• 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets
by
nicklesteele532
• 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions?
by
Hervé Pagès
16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons
by
swbarnes2
★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
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