Showing : Contrast • reset
0
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3
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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
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1
reply
351
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 14 months ago by 39k • written 14 months ago by • 0
2
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3
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646
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 15 months ago by 39k • written 15 months ago by • 0
0
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1
reply
410
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
18 months ago slcno • 0
2
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9
replies
3.4k
views
Contrasts in DESeq2
deseq2 contrast
updated 6 months ago by • 0 • written 2.3 years ago by ▴ 30
3
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2
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434
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LIMMA Time descendant design
limma time-dependant contrast
updated 2.4 years ago by 62k • written 2.4 years ago by ▴ 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 39k • written 2.6 years ago by • 0
1
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1
reply
20k
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lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 3.1 years ago by 39k • written 3.1 years ago by ★ 1.5k
0
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2
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402
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same results changing contrast function
deseq2 contrast DEG
updated 3.2 years ago by 39k • written 3.2 years ago by • 0
0
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4
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1.2k
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DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
3.3 years ago luciest.rodriguez • 0
1
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3
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2.4k
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Multi-factor analysis Deseq2
deseq2 contrast LTR
4.3 years ago • updated 3.4 years ago Iryna • 0
1
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5
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620
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dseq2 results synergy contrast
deseq2 contrast synergy
updated 3.7 years ago by 39k • written 3.7 years ago by ▴ 90
0
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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
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1.0k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2 contrast ratio of ratio
updated 4.0 years ago by 39k • written 4.0 years ago by ▴ 30
3
votes
5
replies
933
views
lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 4.2 years ago by 39k • written 4.2 years ago by ▴ 10
2
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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 47k • written 4.2 years ago by • 0
0
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5
replies
874
views
RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 4.4 years ago by 39k • written 4.4 years ago by ▴ 10
0
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3
replies
640
views
A contrast with four simultaneous conditions for DESeq2?
DESeq2 contrast results
updated 4.6 years ago by 39k • written 4.6 years ago by • 0
1
vote
5
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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
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4
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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 47k • written 5.0 years ago by ▴ 20
9
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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 39k • written 5.1 years ago by ▴ 60
2
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4
replies
924
views
Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 5.2 years ago by 62k • written 5.2 years ago by ▴ 60
0
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4
replies
1.3k
views
Time points and donors - errors with contrasts
deseq2 contrast
updated 5.2 years ago by 39k • written 5.6 years ago by • 0
0
votes
2
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711
views
Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 5.3 years ago by 39k • written 5.3 years ago by ▴ 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 47k • written 5.5 years ago by ▴ 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 39k • written 5.5 years ago by ▴ 10
16
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7
replies
10.0k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 5.5 years ago by 39k • written 5.5 years ago by ▴ 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 ★ 28k • written 5.6 years ago by • 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 39k • written 5.7 years ago by • 0
0
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1
reply
1.1k
views
how to extract complex contrast with DESeq2
contrast DESeq2 differential gene expression
updated 5.8 years ago by 39k • written 5.8 years ago by ▴ 90
0
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7
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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
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1
reply
1.2k
views
intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 5.9 years ago by 39k • written 5.9 years ago by • 0
2
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13
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3.4k
views
DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
6.0 years ago crfitzpat • 0
2
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3
replies
868
views
Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2 contrast
updated 6.0 years ago by 39k • written 6.0 years ago by • 0
0
votes
2
replies
771
views
edgeR constrast drug treatments and time points
edgeR contrast
updated 6.3 years ago by ★ 28k • written 6.3 years ago by ▴ 10
0
votes
3
replies
1.4k
views
limma camera function Multiple contrasts
limma microarray contrast camera
updated 6.4 years ago by 47k • written 6.4 years ago by ▴ 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 ★ 28k • written 6.7 years ago by ▴ 300
1
vote
6
replies
814
views
Are these contrasts correct for use in DESeq2?
deseq2 contrast
updated 6.7 years ago by 39k • written 6.7 years ago by ▴ 90
2
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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 39k • written 6.8 years ago by ▴ 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 39k • written 7.2 years ago by ▴ 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 39k • written 7.3 years ago by ▴ 20
3
votes
5
replies
1.1k
views
pass limma contrast matrix variable
contrast limma
updated 7.4 years ago by 47k • written 7.4 years ago by ▴ 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 39k • written 7.5 years ago by ▴ 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 39k • written 7.6 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
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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