Showing : EDGER • reset
2
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8
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Differential gene expression using edgeR and using a generalised linear model (GLM)
edger GLM
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
2
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4
replies
1.2k
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Why the result of pairwise comparison and Anova comparison of the same contrast is different ?
edger
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 10
1
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1
reply
1.6k
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Meaning of edgeR decideTestsDGE values
edger
updated 6.5 years ago by 53k • written 6.5 years ago by • 0
1
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2
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1.2k
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Call DE genes on Unbalanced design with controls
edger experimental design
6.5 years ago timedreamer ▴ 10
5
votes
5
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4.5k
views
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
limma edger
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 40
2
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4
replies
6.0k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
1
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6
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2.3k
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edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 6.5 years ago by 68k • written 6.5 years ago by ▴ 120
1
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2
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1.1k
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Regarding error in Trinity edgeR calculation
edger
updated 6.5 years ago by 53k • written 6.5 years ago by • 0
1
vote
4
replies
1.8k
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Complex Design matrix for DE analysis
deseq2 edger limma
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
8
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5
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5.0k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 120
0
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2
replies
1.3k
views
How to create design matrix for differential analysis within the same cell-line samples?
edger r differentialanalysis rnaseq designmatrix
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 60
1
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3
replies
1.2k
views
edgeR for looking at differences in coverage?
edgeR exome
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
3
votes
3
replies
2.9k
views
edgeR: Strange volcano plot
edger scRNA-seq DGEA
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
0
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5
replies
2.7k
views
EdgeR: Filtering Counts Causes No Significance.
edger
updated 4.7 years ago by • 0 • written 6.5 years ago by • 0
2
votes
5
replies
3.3k
views
MDS plot; Batch effects
limma rna-seq edger batches
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
0
votes
1
reply
804
views
Help with edgeR
edger
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 10
4
votes
7
replies
1.8k
views
EdgeR between/within comparisons (3.5) with nested non-balanced data set
edgeR nested glm glmQLFit
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 10
3
votes
3
replies
1.7k
views
Voom shows error message:
Limma voom edger
updated 6.6 years ago by 53k • written 6.6 years ago by • 0
2
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6
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2.2k
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EdgeR glmTreat error
edger error
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
0
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2
replies
2.5k
views
create DGElist Object
edger DGElist
updated 6.6 years ago by 53k • written 6.6 years ago by • 0
0
votes
0
replies
989
views
Paired DE analysis in edgeR with trios of samples while blocking for various confounders
edger rnaseq paired analysis design matrix
6.6 years ago svlachavas ▴ 840
6
votes
7
replies
1.8k
views
Appropriate experimental design for differential expresion
edgeR normalization cancer
updated 6.6 years ago by ★ 1.4k • written 6.6 years ago by ▴ 30
3
votes
4
replies
1.6k
views
RNA-seq Statstical Models and Transcriptional Amplification
edgeR DESeq2 Transcriptional Amplification
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ★ 1.6k
3
votes
5
replies
2.0k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 40
1
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3
replies
3.4k
views
ENSEBL gene_ID in edgeR analysis
edgeR ENEMBL RefSeq
updated 6.6 years ago by 53k • written 6.6 years ago by • 0
0
votes
4
replies
2.3k
views
How to analyze RNAseq data with multiple treatment groups and each subject has pre and post-treatment measures using deseq2/edger/limma?
deseq2 limma edger Tutorial
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
4
votes
3
replies
1.9k
views
subset samples for RNAseq differential analysis
edger rnasq limma
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
1
vote
2
replies
1.2k
views
edgeR design matrix not of full rank
edger
updated 6.7 years ago by ★ 29k • written 6.7 years ago by • 0
0
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2
replies
1.0k
views
using limma for circular RNA analyses
limma R edger
updated 6.7 years ago by ★ 29k • written 6.7 years ago by • 0
0
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1
reply
2.1k
views
Dependence of FDR and P-values on sample size
edgeR FDR p-value Benjamini-Hochberg Differential Analysis
updated 6.7 years ago by ★ 29k • written 6.7 years ago by • 0
3
votes
4
replies
1.8k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 10
0
votes
0
replies
1.3k
views
I am trying to recreate results from an Alzheimer's paper but I can't figure out my linear regression model
limma microarray differential gene expression linear regression edger
6.7 years ago ravelarvargas • 0
3
votes
7
replies
1.2k
views
edgeR: request for additional guidelines for responsible limiting of genes that can be analyzed statistically
edger
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
0
votes
4
replies
1.4k
views
Batch effect and edgeR analysis
batch effect edgeR RNA-seq
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 20
1
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2
replies
2.3k
views
Biological coefficient of variation(BCV) calculation in edgeR
edger bcv edgeR
updated 6.7 years ago by ★ 29k • written 6.7 years ago by • 0
1
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4
replies
1.8k
views
I am having trouble recreating the linear regression results published in an Alzheimer's paper
limma edger linear regression microarray differential gene expression
6.7 years ago ravelarvargas • 0
2
votes
10
replies
4.0k
views
Time-series analysis with DESeq2
deseq2 time-series design matrix edger
updated 6.7 years ago by 43k • written 6.7 years ago by ★ 1.5k
2
votes
6
replies
1.7k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
4
votes
4
replies
3.1k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 680
8
votes
4
replies
3.3k
views
edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
hemoglobin edgeR deseq2 normalization rnaseq
updated 6.7 years ago by ★ 7.9k • written 6.7 years ago by ▴ 90
0
votes
1
reply
1.1k
views
differentail expression analysis with interaction terms
edger deseq2 interaction design matrix
updated 6.7 years ago by 68k • written 6.7 years ago by ★ 1.5k
5
votes
3
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1.1k
views
Conduct likelihood ratio tests for a variable that isn't explicitly defined by matrix.model
edger
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
1
vote
3
replies
823
views
How do you obtain the R - squared value from the NB line produced in plotMeanVar ?
edger rnaseq R
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
6
votes
8
replies
3.8k
views
Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
RNASeq-quantification edgeR TPM
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 30
1
vote
5
replies
1.7k
views
My linear regression model is giving me too many differentially expressed genes
limma rna-seq differential gene expression edger linear regression
updated 6.8 years ago by ★ 29k • written 6.8 years ago by • 0
2
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5
replies
2.3k
views
edgeR or wilcoxon rank test? Which is right?
edgeR r wilcox RNA-seq cancer
6.8 years ago AZ ▴ 30
2
votes
6
replies
1.6k
views
Differential expression analysis error
edger
updated 6.8 years ago by 53k • written 6.8 years ago by • 0
1
vote
8
replies
2.2k
views
how can I calculate FDR with no replicate
microarray edger
updated 6.8 years ago by 53k • written 6.8 years ago by ▴ 30
1
vote
2
replies
1.3k
views
EdgeR -- differentially expressed genes across a continuous variable
edger continuous regression
updated 6.8 years ago by 68k • written 6.8 years ago by • 0
3
votes
7
replies
1.8k
views
Different results with DESeq2 and EdgeR
desEQ2 edger
6.8 years ago AZ ▴ 30
2,031 results • Page 13 of 41
Recent ...
Replies
Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis by Michael Love 43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Answer: Integration: Paired-end vs healthy single-end from a different source by James W. MacDonald 68k
If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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