Showing : contrasts • reset
2
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3
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266
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edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
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3
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633
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Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 9 months ago by 65k • written 9 months ago by • 0
1
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2
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545
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Individual DESeq2 runs versus a single DESeq2 run with contrasts produce different results
contrasts DESeq2
10 months ago jovel_juan ▴ 30
3
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6
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969
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Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
1
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3
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652
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Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 17 months ago by 50k • written 17 months ago by • 0
3
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8
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3.3k
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DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 23 months ago by ▴ 10
0
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3
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1.2k
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limma voom contrasts
contrasts limma voom
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 90
0
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1
reply
710
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DESeq2 2x3 design contrast question
DESeq2 contrasts
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
0
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2
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951
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.6 years ago James • 0
0
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3
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988
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DESeq2: difficulty with contrasts and main effects
DESeq2 phyloseq contrasts
updated 2.7 years ago by ★ 3.9k • written 2.7 years ago by • 0
2
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8
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2.0k
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
2.9 years ago Jane ▴ 10
3
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8
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1.2k
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Same contrasts returning different edgeR results
edger limma contrasts DGE
updated 4.3 years ago by 65k • written 4.3 years ago by • 0
0
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1
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1.0k
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DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 4.4 years ago by 41k • written 4.4 years ago by • 0
0
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0
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670
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EdgeR: Transforming coefficients before testing for differential expression
edger contrasts model.matrix circadian
4.4 years ago ingerslev • 0
0
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1
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1.1k
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DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 4.4 years ago by 41k • written 4.4 years ago by • 0
2
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3
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1.4k
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DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2 deseq differential expression contrasts
updated 4.4 years ago by 41k • written 4.4 years ago by ▴ 180
0
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4
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964
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Setting up contrasts with 'limma', patient data, small number of repeats
limma nanostring contrasts
updated 4.6 years ago by 50k • written 4.6 years ago by • 0
0
votes
1
reply
670
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DESeq2 compairson of 3 samples from 1 type
deseq2 multiple factor design contrasts experimental design
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
3
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5
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1.4k
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Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
2
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6
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1.1k
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Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 5.2 years ago by 50k • written 5.2 years ago by • 0
20 results • Page 1 of 1
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Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850
This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…
Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k
Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…
Answer: Adding columns to DEXSeqResults object by Alejandro Reyes ★ 1.9k
I'd have a look into the match function, that could give you a mapping between the ids in the dxr1 object and your data frame of gene symbo…
Votes
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
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