Showing : edgeR • reset
0
votes
3
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2.0k
views
Error to convert a DGEList to DESeqDataSet in DEFormats
DEFormats DESeq2 edger
9.3 years ago Akira Imamoto • 0
3
votes
3
replies
7.6k
views
QLF or LRT in edgeR for paired sample designs?
edger paired samples glm QL F-test LR-test
written 9.3 years ago by • 0
1
vote
12
replies
2.2k
views
Help for defining design and contrasts of shRNA screen data
edgeR design and contrast matrix
updated 9.3 years ago by ★ 29k • written 9.3 years ago by ▴ 90
3
votes
6
replies
2.5k
views
Clarification MAplot and FDR in EdgeR
edgeR MAplot rnaseq differential gene expression
updated 9.3 years ago by 53k • written 9.3 years ago by • 0
1
vote
7
replies
3.8k
views
RNA-seq: two factor anova - how to find the variability explained by each of the factor?
rnaseq two factor anova limma DEseq2 edgeR
9.3 years ago nooshin ▴ 300
2
votes
2
replies
1.2k
views
variance-covariance matrix edgeR
edger
updated 9.3 years ago by 53k • written 9.3 years ago by ▴ 180
8
votes
3
replies
4.9k
views
Appropriate ways to filter counts data for voom/limma
limma edger sequencing
written 9.3 years ago by ▴ 10
0
votes
2
replies
995
views
readDGE function error in R
edger
updated 9.3 years ago by ★ 29k • written 9.3 years ago by • 0
4
votes
6
replies
3.3k
views
How to carry out differential gene expression starting with a table of TMM normalised values without access to the raw reads?
edger raw reads TMM normalised values DGEList differential gene expression
updated 9.3 years ago by ★ 13k • written 9.3 years ago by ▴ 30
1
vote
2
replies
1.8k
views
Should edgeR-GLM on single cell RNA data be performed on the counts or normalized data?
edger scran
updated 9.3 years ago by ▴ 90 • written 9.3 years ago by • 0
2
votes
7
replies
3.2k
views
About differentially expressed genes that found by edgeR
edgeR DE analysis fold change cpm
updated 9.3 years ago by ★ 7.9k • written 9.3 years ago by ▴ 20
0
votes
8
replies
2.5k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
9.3 years ago a.guerra • 0
4
votes
15
replies
2.5k
views
Please share me your helpful comments with edgeR analysis without replicate
edgeR dispersion value replication
updated 9.3 years ago by 53k • written 9.3 years ago by ▴ 20
1
vote
1
reply
920
views
New version with problem for estimation of dispersion
edger
updated 9.3 years ago by ★ 29k • written 9.3 years ago by • 0
1
vote
4
replies
2.3k
views
problems when installing edgeR
edgeR limma
updated 9.3 years ago by 53k • written 9.3 years ago by • 0
16
votes
6
replies
4.2k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR limma diffSplice DEXSeq
updated 9.3 years ago by ▴ 90 • written 9.3 years ago by ▴ 180
1
vote
3
replies
1.5k
views
Please help with estimating dispersion value using housekeeping genes in edgeR
estimate dispersion value edgeR Houskeeping genes
updated 9.3 years ago by ★ 7.9k • written 9.3 years ago by ▴ 20
5
votes
4
replies
2.7k
views
Why does the filtering of lowly expressed genes for analysis with edgeR must be done unsupervised?
edgeR RNAseq DE analysis gene filtering
9.3 years ago Mau ▴ 50
2
votes
2
replies
2.4k
views
Analysis of shRNA screen data
shrna edger deseq2 differential expression normalized counts
9.3 years ago Jane Merlevede ▴ 90
1
vote
9
replies
2.7k
views
RPKM normalization for several samples using a for loop
edger forloop
updated 4.6 years ago by 53k • written 9.3 years ago by • 0
3
votes
7
replies
7.7k
views
edgeR subsetting DGEList by column/sample
edger subsetting dgelist
updated 9.3 years ago by 53k • written 9.3 years ago by ▴ 10
3
votes
5
replies
2.7k
views
Using Scran normalization with in edgeR
edger estimatedisp scran sizefactors
updated 9.4 years ago by ★ 29k • written 9.4 years ago by ▴ 10
4
votes
3
replies
1.8k
views
What is the correct contrast matrix if one treatment must be compared to both of the other two treatments, but separately?
edger limma model.matrix contrast matrix design matrix
updated 9.4 years ago by ▴ 690 • written 9.4 years ago by • 0
3
votes
1
reply
6.6k
views
edgeR: exactTest, glmFIt or glmQLFit approach?
edger rnaseq glm glmfit
updated 9.4 years ago by ★ 29k • written 9.4 years ago by • 0
2
votes
2
replies
1.5k
views
edgeR: why the codes with and without coef=2 produce different results?
edgeR
updated 9.4 years ago by 53k • written 9.4 years ago by • 0
0
votes
7
replies
3.9k
views
Repeated Measures mRNA expression analysis II
limma edgeR DESeq
updated 9.4 years ago by • 0 • written 12.4 years ago by ▴ 140
7
votes
11
replies
7.0k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR limma annotationhub kegga annotationdbi
updated 9.4 years ago by ▴ 20 • written 9.7 years ago by ▴ 20
3
votes
10
replies
8.5k
views
Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : newsplit: out of vertex space in paired edgeR comparison
edger paired samples model.matrix estimatedisp
updated 9.4 years ago by 53k • written 9.4 years ago by ▴ 30
3
votes
4
replies
2.2k
views
Competitive gene set testing between two sets of genes
gene set testing camera edger
updated 9.4 years ago by 53k • written 9.4 years ago by ▴ 20
9
votes
16
replies
8.9k
views
edger, trended or common dispersion
edger
updated 9.4 years ago by ▴ 20 • written 9.9 years ago by ▴ 80
9
votes
12
replies
11k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
written 9.5 years ago by ▴ 20
0
votes
1
reply
2.5k
views
DiffBind TMM normalization
Rory Stark diffbind TMM edgeR chipseq
updated 9.4 years ago by ★ 5.2k • written 9.5 years ago by • 0
2
votes
11
replies
2.4k
views
Adjusting for confounders along with paired testing using edgeR
edgeR paired samples confounders model.matrix
updated 9.4 years ago by ★ 7.9k • written 9.4 years ago by ▴ 30
4
votes
5
replies
3.1k
views
edgeR- DE analysis with no replicates
edger differential gene expression without replicate nested design help
updated 9.4 years ago by ★ 29k • written 9.4 years ago by • 0
2
votes
1
reply
1.2k
views
edgeR - testing interaction in a scenario of 2 tissues and 2 ages
edgeR R differential gene expression differential expression
updated 9.4 years ago by ★ 29k • written 9.4 years ago by • 0
0
votes
3
replies
2.7k
views
Standard errors of fitted values from glmFit in edgeR
edger standard error glmfit
9.4 years ago david.hughes • 0
15
votes
4
replies
3.7k
views
Using multiple tools for differential gene expression analysis as validation
edger limma deseq2 rnaseq
updated 9.4 years ago by ★ 7.9k • written 9.4 years ago by ▴ 130
8
votes
5
replies
12k
views
EdgeR glmLRT vs glmQLFTest
bioconductor edger
updated 9.4 years ago by ★ 13k • written 9.4 years ago by • 0
14
votes
5
replies
9.0k
views
EDGE-R exact test vs QL F-test
edger rnaseq
updated 3.6 years ago by • 0 • written 9.4 years ago by ▴ 40
12
votes
2
replies
4.2k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 9.4 years ago by 53k • written 9.4 years ago by ▴ 80
6
votes
4
replies
5.6k
views
Does DESeq2 or edgeR take care of random effect in the GLM
deseq2 edger
updated 9.4 years ago by 53k • written 9.4 years ago by ▴ 120
3
votes
6
replies
2.0k
views
Question about edgeR usage with one case and multiple controls
edgeR differential expression without replicate
9.4 years ago gavin.oliver • 0
1
vote
4
replies
2.3k
views
Effect of treatment vs control over time in RNA Seq (edgeR and limma)
edgeR limma voom RNASeq multiple time points
updated 9.4 years ago by ★ 7.9k • written 9.4 years ago by ▴ 20
3
votes
1
reply
3.1k
views
Gene level exploratory data analysis from tximport results
tximport edgeR DESeq2
updated 9.4 years ago by 43k • written 9.4 years ago by ★ 13k
1
vote
2
replies
1.8k
views
Common dispersion from estimateGLMRobustDisp()
edgeR dispersion
updated 9.4 years ago by ★ 29k • written 9.4 years ago by ▴ 90
1
vote
2
replies
1.1k
views
Issue with edgeR
software error edger columns
updated 9.4 years ago by 53k • written 9.4 years ago by • 0
2
votes
8
replies
3.7k
views
Problem using the readDGE function
readDGE edgeR
updated 9.4 years ago by 53k • written 9.4 years ago by • 0
6
votes
4
replies
2.1k
views
How to normalize chemical genomics barcode sequencing data
limma normalization sequencing edger
updated 9.4 years ago by ★ 29k • written 9.4 years ago by ▴ 20
2
votes
2
replies
1.8k
views
Sample sizes must be equal for TMM?
TMM edgeR
9.4 years ago humberto_munoz • 0
2
votes
6
replies
7.1k
views
edgeR installation issue
software error edger
9.4 years ago t3h096 • 0
2,031 results • Page 23 of 41
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