Showing : Contrast • reset
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Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 7 weeks ago by 35k • written 7 weeks ago by • 0
2
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3
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234
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Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 3 months ago by 35k • written 3 months ago by • 0
0
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1
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186
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
6 months ago • updated 5 months ago slcno • 0
2
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6
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412
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Contrasts in DESeq2
deseq2 contrast
updated 15 months ago by 35k • written 15 months ago by ▴ 20
3
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2
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285
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LIMMA Time descendant design
limma time-dependant contrast
updated 16 months ago by 58k • written 16 months ago by ▴ 10
5
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10
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483
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Correctly set contrast with DESeq2 for not full rank design matrix
DESeq2 DGE contrast
updated 19 months ago by 35k • written 19 months ago by • 0
1
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1
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8.8k
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lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 2.0 years ago by 35k • written 2.0 years ago by ★ 1.5k
0
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2
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244
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same results changing contrast function
deseq2 contrast DEG
updated 2.2 years ago by 35k • written 2.2 years ago by • 0
0
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4
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859
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DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
2.3 years ago luciest.rodriguez • 0
1
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3
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1.5k
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Multi-factor analysis Deseq2
deseq2 contrast LTR
3.2 years ago • updated 2.4 years ago Iryna • 0
1
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5
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349
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dseq2 results synergy contrast
deseq2 contrast synergy
updated 2.7 years ago by 35k • written 2.7 years ago by ▴ 90
0
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9
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734
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NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq deseq2 contrast subgroup
2.9 years ago ariel ▴ 10
2
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7
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612
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DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2 contrast ratio of ratio
updated 2.9 years ago by 35k • written 2.9 years ago by ▴ 30
3
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5
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618
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lfcShrink, interactions, and ashr
deseq2 lfcshrink contrast
updated 3.1 years ago by 35k • written 3.1 years ago by ▴ 10
2
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1
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368
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EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
edgeR design matrix contrast
updated 3.2 years ago by 44k • written 3.2 years ago by • 0
0
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5
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608
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RNA-seq time course experiment - DESEq2 Contrasts
deseq2 rna-seq interactions contrast
updated 3.3 years ago by 35k • written 3.3 years ago by ▴ 10
0
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3
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484
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A contrast with four simultaneous conditions for DESeq2?
DESeq2 contrast results
updated 3.6 years ago by 35k • written 3.6 years ago by • 0
1
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5
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1.2k
views
DESeq2 Subsetting gives error in contrasts - can be applied only to factors with 2 or more levels
deseq2 multiple factor design contrast
3.6 years ago russell.stewart.j • 0
2
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4
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4.5k
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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 4.0 years ago by 44k • written 4.0 years ago by ▴ 20
7
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1
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1.7k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 4.0 years ago by 35k • written 4.0 years ago by ▴ 60
2
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4
replies
728
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Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 4.1 years ago by 58k • written 4.1 years ago by ▴ 60
0
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4
replies
1.1k
views
Time points and donors - errors with contrasts
deseq2 contrast
updated 4.2 years ago by 35k • written 4.5 years ago by • 0
0
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2
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548
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Discrepancy in extracting contrasts
deseq2 resultsnames batch effect contrast
updated 4.3 years ago by 35k • written 4.3 years ago by ▴ 10
2
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5
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1.4k
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 4.4 years ago by 44k • written 4.4 years ago by ▴ 10
0
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2
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1.1k
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DESEq2 contrast statement syntax and design statement question
deseq2 interactions contrast
updated 4.4 years ago by 35k • written 4.4 years ago by • 0
12
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7
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7.8k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 4.5 years ago by 35k • written 4.5 years ago by ▴ 10
2
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2
replies
1.4k
views
EdgeR -ANOVA-like test vs testing individual contrasts
EdgeR ANOVA t-test contrast
updated 4.6 years ago by ★ 27k • written 4.6 years ago by • 0
0
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5
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2.6k
views
DESEQ2 'results' filter by value for multiple conditions (contrast off?)
deseq2 results contrast padj
updated 4.6 years ago by 35k • written 4.6 years ago by • 0
0
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1
reply
911
views
how to extract complex contrast with DESeq2
contrast DESeq2 differential gene expression
updated 4.7 years ago by 35k • written 4.7 years ago by ▴ 70
0
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7
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1.9k
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Computing contrasts with a covariate using edgeR glmLRT()
edger contrast covariate glmlrt()
4.8 years ago Jeff Skinner • 0
3
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19
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2.1k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
4.8 years ago mheydarpour ▴ 10
0
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1
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1.1k
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intra-sample time series comparison using DESeq2
deseq2 time course rnaseq design contrast
updated 4.9 years ago by 35k • written 4.9 years ago by • 0
2
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13
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2.6k
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DESeq2 log fold change estimates for factors with many levels
deseq2 lfce contrast
4.9 years ago crfitzpat • 0
2
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3
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686
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Using contrast argument of DESeq2 to estimate linear combination coefficients
deseq2 contrast
updated 4.9 years ago by 35k • written 4.9 years ago by • 0
0
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2
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626
views
edgeR constrast drug treatments and time points
edgeR contrast
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 10
0
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3
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1.3k
views
limma camera function Multiple contrasts
limma microarray contrast camera
updated 5.3 years ago by 44k • written 5.3 years ago by ▴ 20
2
votes
6
replies
839
views
edgeR - making 12 contrast but only get 5 contrasts as a result
r edger de contrast design and contrast matrix
updated 5.6 years ago by ★ 27k • written 5.6 years ago by ▴ 300
1
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6
replies
652
views
Are these contrasts correct for use in DESeq2?
deseq2 contrast
updated 5.7 years ago by 35k • written 5.7 years ago by ▴ 90
2
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2
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1.4k
views
"U" shaped p values distribution in DESeq2 RNA-seq DE analysis using the contrast argument
deseq2 rnaseq contrast multiple comparisons fdrtool
5.7 years ago sebastiano.curreli • 0
2
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6
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1.1k
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 5.8 years ago by 35k • written 5.8 years ago by ▴ 10
2
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4
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3.6k
views
Interaction terms in DESeq2 contrasts
deseq2 interactions design and contrast matrix contrast
5.8 years ago dwzhang.wisc ▴ 20
0
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5
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3.9k
views
DESeq2 multifactor experiment design
deseq2 LRT multifactor contrast interactions
6.0 years ago rclaire • 0
6
votes
1
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1.8k
views
DESeq2, difficulties with multi-factor design
DESeq2 multiple factor design experimental design contrast
updated 6.2 years ago by 35k • written 6.2 years ago by ▴ 60
4
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9
replies
1.2k
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How to construct contrasts for a linear model with interactions?
limma contrast linear model
6.2 years ago vedran.franke • 0
1
vote
4
replies
827
views
Specificity of gene expression
differential gene expression specific expression contrast deseq2
6.3 years ago arrigonialberto86 • 0
0
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1
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1.2k
views
DESeq2 design issues - specifically understanding contrasts & interactions from page 23-25 of the DESeq2 manual
deseq2 design and contrast matrix interactions contrast
updated 6.3 years ago by 35k • written 6.3 years ago by ▴ 20
3
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5
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970
views
pass limma contrast matrix variable
contrast limma
updated 6.3 years ago by 44k • written 6.3 years ago by ▴ 210
6
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2
replies
3.5k
views
All same padj of contrast results in the DESeq2
deseq2 padj contrast results
updated 6.4 years ago by 35k • written 6.4 years ago by ▴ 20
7
votes
9
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3.0k
views
DESeq2: Compare expression of one group to the mean of others
deseq2 heterosis contrast design and contrast matrix
updated 6.6 years ago by 35k • written 6.6 years ago by ▴ 10
2
votes
8
replies
2.4k
views
confusing on the interaction and betaprior in DESeq2.
deseq2 interactions contrast
6.6 years ago shao ▴ 90
50 results • Page 1 of 1
Recent ...
Replies
Comment: Gviz and datatracks by Malcolm Cook ★ 1.5k
what is the value of bgFile? It probably does not have an extension the DataTrack recognizes....
Answer: Large DE LogFC range by Michael Love 35k
Agree with ATpoint, look at the genes with large LFC (from lfcShrink) using `plotCounts`. Usually large MLE LFC are from all 0's in one gro…
Comment: Large DE LogFC range by ATpoint ▴ 970
You could at least show some counts of the genes with large FCs. Also the PCA would help.
Comment: Weird output of DESeq2 when using single sample from one group agains the other by Michael Love 35k
See the 2014 paper, the MLE LFC is found via IRLS: "We use the standard iteratively reweighted least-squares algorithm [12] for each gene’…
Comment: Weird output of DESeq2 when using single sample from one group agains the other by FantasticAI • 0
Thank you for the help. Sorry for keep asking silly questions: I wonder given 2 groups (A and B), and each group has 6 samples, how does th…
Votes
Where can I find EnsDb.Hsapiens.v105?
Two-way interaction, linear redundancy
Answer: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
Answer: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
Answer: Joint disperstion estimation for DEXSeq and DESeq2
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