Showing : rna • reset
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Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA RNASeqPower DEGseq
written 3 months ago by • 0
0
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3
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650
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Trouble with creating Series RNA-seq normalized counts matrix
GEO rnaseqGene RNA
7 months ago gallantk5 • 0
0
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5
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1.3k
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Help with DESeq results to pathways with the fgsea package
fgsea rna
updated 12 months ago by 68k • written 12 months ago by • 0
0
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1
reply
661
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Running Deseq2 with all samples vs samples for each comparison separately
RNA DESeq2
updated 13 months ago by 43k • written 13 months ago by • 0
0
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2
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1.7k
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Access Ensembl GRCH38 Version 87 Using BiomaRt
biomaRt ensembldb RNA ensembl
updated 23 months ago by ★ 2.1k • written 23 months ago by • 0
3
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6
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2.9k
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Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
2.3 years ago Sara • 0
0
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0
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745
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Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
2.4 years ago rridley3 • 0
1
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1
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1.0k
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Confused about design for RNA seq experiment
RNAseq ExperimentData RNAseq123 RNA ExperimentalDesign
updated 2.5 years ago by ★ 4.7k • written 2.5 years ago by ▴ 30
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0
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984
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Job: Scientist/Senior Scientist – Bioinformatics / Computational Biology
MassSpectrometryData RNA DifferentialExpression
2.5 years ago António Miguel de Jesus Domingues ▴ 510
0
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2
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1.1k
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Rsubread align --R session aborts
RNA Alignment Rsubread
2.6 years ago • updated 2.5 years ago sreekalasn • 0
2
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1
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1.4k
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Error in RNAseq123 analysis, unexpected symbol.
RNAseq123 Rna
updated 2.7 years ago by 52k • written 2.7 years ago by • 0
1
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2
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2.2k
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Is it necessary to standardize Combat in R?
RNA Combat sva R
2.8 years ago takemoto • 0
1
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1
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1.0k
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Description of the headers obtained from the Eligos2 output
methylation RNA native epitranscriptomics
updated 3.0 years ago by ▴ 100 • written 3.0 years ago by ▴ 10
0
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1
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1.1k
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Ensembl dataset version
tximport rna rnaseqGene biomaRt
updated 3.2 years ago by ★ 4.7k • written 3.2 years ago by • 0
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0
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834
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Cross-cultivar RNA-seq analysis
RNA Normalization
3.9 years ago nancy • 0
0
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4
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1.8k
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Fitting a continuous variable with batch effect using Limma. Also a question about normalization.
limma edgeR rna
3.9 years ago Nirad ▴ 10
0
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3
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2.8k
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Pearson correlation between gene expression and phenotype
edgeR RNASeq
updated 4.3 years ago by 52k • written 4.3 years ago by ▴ 10
4
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3
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3.1k
views
How to resolve NAs when annotating a diff gene list with org.Hs.eg.db terms?
annotation rna
updated 4.4 years ago by 68k • written 4.4 years ago by ▴ 20
2
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7
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1.6k
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Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy rna hta2.0 r
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
1
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1
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1.1k
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How to interpret coefficients of time course modeled data with DESeq2?
deseq2 RNA
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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6
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1.8k
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Bizarre Dispersion Plots
deseq2 RNA RNASeq
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
0
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0
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1.1k
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Job: Post-doctoral Fellowship at BC Cancer Research Center, Vancouver BC
single cell RNA Data analysis Bioinformatics Job
5.6 years ago jmaanaki • 0
1
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1
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1.7k
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how to filter genes in significant module?
RNA WGCNA filter
5.7 years ago modarzi ▴ 10
0
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2
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1.1k
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DESeq and checkFullRank(modelMatrix)
RNA DESeq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
2
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1
reply
1.0k
views
DESeq2 statistic and design
deseq2 RNA
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 10
5
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5
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1.8k
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Association analysis between gene expression and Phenotype
rna singlecell limma
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 20
2
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3
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1.8k
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Number and percent of mapped reads from RNA seq analysis.
rna-seq rna
updated 5.9 years ago by ★ 13k • written 5.9 years ago by ▴ 20
1
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0
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1.2k
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Job: 1 Computational Biologist and 1 Molecular Biologist
computational biology molecular biology RNA r-loop ncRNA Job
6.4 years ago l.brown ▴ 10
0
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0
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1.2k
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R code for finding wobble/redundant positions in an RNA string
r code rna wobble
7.1 years ago fawazfebin ▴ 60
0
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1
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1.2k
views
Time series comparison with DESEQ2
RNA rnaseq deseq2
updated 7.5 years ago by 43k • written 7.5 years ago by ▴ 20
0
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1
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1.6k
views
RNA sequencing analysis for time point experiment using DeSeq2
deseq2 RNA rnaseq
updated 7.6 years ago by 43k • written 7.6 years ago by ▴ 20
1
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1
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2.1k
views
Outliers - to remove or to not remove that is the question
outliers rna microarray
updated 7.8 years ago by ▴ 420 • written 7.8 years ago by ▴ 30
5
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4
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1.6k
views
Experiment design contrasts any time edgeR
DGE rnaseq RNA edger
updated 7.8 years ago by • 0 • written 7.8 years ago by ▴ 40
3
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6
replies
2.2k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 7.9 years ago by 68k • written 7.9 years ago by ▴ 20
6
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5
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4.5k
views
Clustering differential expression results from voomWithQualityWeights
RNA limma rsem edgeR
updated 7.9 years ago by 52k • written 7.9 years ago by ▴ 20
0
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0
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1.7k
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Finding candidate binding sites for RNA binding proteins in R
R bioconductor RNA mRNA RNA binding proteins
8.0 years ago Walter F. Baumann ▴ 10
3
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1
reply
1.9k
views
Targeted RNASeq/CaptureSeq DE Analysis
EdgeR deseq2 RNA differential expression
updated 8.5 years ago by ★ 28k • written 8.5 years ago by • 0
0
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4
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5.3k
views
RNAseq Adjusting for Covariates?
RNA rnaseq Covariate adjustment deseq
updated 9.0 years ago by 43k • written 9.0 years ago by • 0
0
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2
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1.5k
views
Normalizzation indipentent data from RNAAeq experiment
rna normalization
10.4 years ago aristotele_m ▴ 40
39 results • Page 1 of 1
Recent ...
Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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