Showing : differential expression • reset
2
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9
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Limma: Defining the design matrix of a linear mixed model
rnaseq limma differential expression
7.3 years ago • updated 7.2 years ago j.baldauf • 0
3
votes
4
replies
2.5k
views
How to find significantly stably expressed miRNA with DESeq2 DE results
deseq2 microrna differential expression stable expression
8.5 years ago mariakarand ▴ 20
22
votes
17
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7.1k
views
DESeq2 1.20.0 lfcshrink function
deseq2 differential expression logfoldchange lfcshrink lfcthreshold
updated 2.9 years ago by 41k • written 5.8 years ago by ▴ 30
6
votes
4
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2.6k
views
discrepance in DESeq2 results with different design structures
deseq2 differential expression independent filtering pre-filtering design matrix
9.0 years ago Assa Yeroslaviz ★ 1.5k
1
vote
5
replies
7.4k
views
DESeq2 and edgeR getting very different results
edger deseq2 differential expression
updated 6.4 years ago by ▴ 20 • written 6.4 years ago by • 0
8
votes
11
replies
2.4k
views
dream vignette says limma-voom repeated measures two-group comparison needs two duplicateCorrelation rounds which differs from limma user's guide and…
dream variancePartition limma differential expression repeated measures
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 20
4
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4
replies
3.4k
views
DESeq2: Abnormally skewed distribution of p-values
deseq2 p-value distribution differential expression
8.7 years ago GFM ▴ 20
3
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5
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6.6k
views
Ballgown up and down regulated genes
ballgown differential expression
updated 7.0 years ago by • 0 • written 8.3 years ago by ▴ 10
5
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4
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1.2k
views
Finding genes respond differently to treatment between many genotype comparison
edgeR nested design differential expression
updated 6.0 years ago by 50k • written 6.0 years ago by • 0
5
votes
3
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4.0k
views
edgeR - how to convert DGELRT and other classes to .csv files
edgeR differential expression file conversion
updated 23 months ago by • 0 • written 8.2 years ago by ▴ 10
2
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5
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1.2k
views
Comparing across sets of regulated genes -- Strategies?
limma differential expression
updated 7.2 years ago by ▴ 730 • written 7.2 years ago by ▴ 30
3
votes
4
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2.9k
views
Protein differential Expression analysis
differential expression proteomics
updated 8 months ago by ★ 4.0k • written 6.3 years ago by • 0
4
votes
4
replies
1.4k
views
Differential expression on codelink data
r codelink differential expression
updated 8.9 years ago by ▴ 760 • written 8.9 years ago by ▴ 260
6
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5
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2.3k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR tximport differential expression
4.0 years ago • updated 3.9 years ago hollandademello ▴ 20
2
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2
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685
views
edgeR - Correct approach to compare abundances of genomic regions?
edger differential expression
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 20
3
votes
6
replies
1.2k
views
Question about edgeR usage with one case and multiple controls
edgeR differential expression without replicate
7.9 years ago gavin.oliver • 0
2
votes
7
replies
2.1k
views
Get the countsFromAbundance as limma input
tximport limma deseq2 differential expression
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
1
vote
3
replies
1.4k
views
Differential expressiong with two groups in BASiCS
BASiCS single-cell bayesian differential expression
updated 6.2 years ago by ▴ 10 • written 6.2 years ago by ▴ 10
6
votes
6
replies
1.8k
views
Can i set a path for readCodlinkSet()
r differential expression codelink
updated 8.8 years ago by ▴ 760 • written 8.9 years ago by ▴ 260
4
votes
6
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2.5k
views
Find if a covariate has effect on gene expression level using edgeR and DESeq2
edger deseq2 model matrix differential expression
7.6 years ago ta65 • 0
2
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2
replies
1.8k
views
Analysis of shRNA screen data
shrna edger deseq2 differential expression normalized counts
7.8 years ago Jane Merlevede ▴ 90
0
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3
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1.4k
views
Differential Expression of c.diff. microarray
arrayexpress differential expression
9.0 years ago SSK ▴ 10
4
votes
5
replies
3.2k
views
How does limma calculate the log2fc?
Limma Differential Expression Time-course Analysis
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 10
1
vote
6
replies
3.4k
views
Two-way anova 2x2 design with limma
limma microarray differential expression
6.5 years ago • updated 6.4 years ago damoros • 0
3
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4
replies
5.1k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
6.6 years ago David Requena ▴ 20
0
votes
17
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3.4k
views
What causes this DESeq2 error at "fitting model and testing"?
deseq2 differential expression error
updated 10 months ago by • 0 • written 6.6 years ago by • 0
5
votes
6
replies
1.2k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 4.7 years ago by ▴ 840 • written 4.7 years ago by ▴ 10
0
votes
1
reply
739
views
Find differentially expressed values
differential gene expression differential expression edgeR
updated 9.0 years ago by 50k • written 9.0 years ago by • 0
1
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1
reply
2.5k
views
EdgeR:Calculating differential expression within/between groups in nested designs
edger nested design matrix differential expression
updated 9.2 years ago by ★ 28k • written 9.2 years ago by • 0
3
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3
replies
1.5k
views
edgeR contrast formulation question
edger rnaseq differential expression
updated 8.6 years ago by ★ 7.9k • written 8.6 years ago by • 0
2
votes
1
reply
1.8k
views
Drastic DE result discrepancies between versions of DESeq2
deseq2 differential expression microbiome
updated 8.6 years ago by 41k • written 8.6 years ago by • 0
1
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4
replies
1.2k
views
Specifically expressed genes
DESeq2 specific expression rnaseq clustering differential expression
updated 9.0 years ago by 41k • written 9.0 years ago by • 0
1
vote
3
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1.4k
views
How different ploidy affect differential expression analysis with RNA-seq
ploidy normalization rna-seq differential expression assumption
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 90
5
votes
2
replies
7.2k
views
Ballgown vs (voom,edgeR,DESeq,limma)
limma rnaseq differential expression voom
updated 9.3 years ago by ▴ 210 • written 9.3 years ago by ▴ 50
1
vote
1
reply
1.3k
views
expression profiles between DESeq2 and Mfuzz
deseq2 mfuzz differential expression timecourse
updated 7.6 years ago by 41k • written 7.6 years ago by ★ 1.5k
3
votes
1
reply
1.6k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 7.6 years ago by ★ 28k • written 7.6 years ago by • 0
2
votes
4
replies
8.5k
views
Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma differential expression design matrix error eset
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
1
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2
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1.9k
views
How to proceed with different degradation levels of RNA-seq samples?
degradation RNA-seq variability differential expression brain
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 90
3
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2
replies
6.2k
views
Trying to understand differential gene expression through Venn Diagrams from the 'limma' R package: why is there a number outside my diagram?
limma r venn diagram differential expression
updated 9.5 years ago by 65k • written 9.5 years ago by • 0
7
votes
10
replies
5.7k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 6.1 years ago by ▴ 30 • written 7.8 years ago by ▴ 50
4
votes
8
replies
1.9k
views
EdgeR: batches and samples over-specify system, how to contrast un-modeled variables?
edger glmlrt() differential expression design and contrast matrix
updated 8.9 years ago by 50k • written 8.9 years ago by • 0
1
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2
replies
1.0k
views
2-Factor Experiment in edgeR, Effect of no reps in one set and two reps in others
rnaseq edger differential expression dispersion
updated 7.5 years ago by ★ 7.9k • written 7.5 years ago by • 0
3
votes
5
replies
1.9k
views
DESeq2: Appropriate way to deal with knockouts in experiment design (RIPSeq)
deseq2 differential expression immunoprecipitation
updated 7.8 years ago by 41k • written 7.8 years ago by ▴ 40
2
votes
1
reply
892
views
edgeR - testing interaction in a scenario of 2 tissues and 2 ages
edgeR R differential gene expression differential expression
updated 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
17
votes
4
replies
30k
views
RPKM, CPM and TMM
edger rnaseq differential expression
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 150
5
votes
3
replies
3.1k
views
Error when calculating DE using the classical approach in edgeR
edgeR differential expression rna-seq
updated 7.6 years ago by 50k • written 7.6 years ago by • 0
1
vote
2
replies
1.6k
views
Passing contrasts as a vector gives an error
r limma differential expression
updated 8.9 years ago by 50k • written 8.9 years ago by ▴ 260
3
votes
10
replies
3.9k
views
Differential expression analysis of already normalized sequence counts
differential expression normalization deseq2
updated 7.9 years ago by 41k • written 7.9 years ago by ▴ 20
4
votes
4
replies
2.5k
views
Two-class unpaired test using LIMMA
Limma SAM differential expression
updated 9.4 years ago by 65k • written 9.4 years ago by ▴ 310
2
votes
3
replies
3.3k
views
Analysis of RNA-seq time series with edgeR
edger rna-seq differential expression timecourse time course
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
50 results • Page 1 of 1
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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