Showing : GeneExpression • reset
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Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools BiomedicalInformatics GeneExpression
updated 10 months ago by 68k • written 10 months ago by • 0
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668
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 11 months ago by ★ 5.0k • written 12 months ago by • 0
2
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1
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570
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Using Affymetrix Custom Array
ArrayExpress makecdfenv AffymetrixChip gcrma GeneExpression
updated 14 months ago by 68k • written 14 months ago by • 0
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565
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 14 months ago by 43k • written 14 months ago by • 0
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9
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1.4k
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
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3
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1.1k
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
22 months ago jbgnielson • 0
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1.1k
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
2.2 years ago Manthos • 0
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3
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5.1k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
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1
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1.3k
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
2.5 years ago Arianna • 0
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2
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4.1k
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FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
2.7 years ago CDSPARKS ▴ 30
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1.2k
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Heatmap of two conditions from the normalized gene count data
GeneExpression heatmaps
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
0
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1
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5.0k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
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4
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3.1k
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Comparing different method for DESEQ2
DESeq2 GeneExpression
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
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3
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1.7k
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CountOverlap
GeneExpression ChIPSeqData
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 20
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810
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Free Gibbson energy RNA doublex
GeneExpression RNAinteract
3.4 years ago Tamina • 0
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1.0k
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
3.5 years ago hlee ▴ 10
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2
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1.5k
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Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression GeneExpression R enrichment DEGseq
updated 3.5 years ago by ★ 1.4k • written 3.5 years ago by • 0
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1
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1.0k
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Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
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1
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1.1k
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Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
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1
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1.2k
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Error while using champ.SVD function
GeneExpression
updated 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
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1
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2.6k
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GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 3.3 years ago by • 0 • written 3.7 years ago by • 0
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0
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1.4k
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Volcano plot: Putting calculated values in legend
GeneExpression
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
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2
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1.3k
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Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 3.8 years ago by • 0 • written 3.9 years ago by ▴ 10
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2
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3.0k
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
4.3 years ago p.l.chen • 0
2
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2
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9.7k
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Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by ▴ 10
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2
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1.6k
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Gene expression in R
limma edgeR Biobase GeneExpression
4.4 years ago sogol.bouyeh • 0
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2
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2.4k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
4.6 years ago SUMIT • 0
5
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18
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4.4k
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DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow DESeq2 GeneExpression
updated 4.7 years ago by 43k • written 4.7 years ago by • 0
1
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3
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1.5k
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DESeq analysis with Biological replicate.
DESeq2 ExpressionData GeneExpression
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
1
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1
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1.0k
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Accounting for fish body mass in DE?
GeneExpression edgeR
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
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1
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1.2k
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Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 5.1 years ago by ▴ 510 • written 5.1 years ago by • 0
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3
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1.5k
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Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression R limma MultipleComparison
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
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960
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
5.2 years ago coobzie • 0
2
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5
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14k
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Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2 r fpkm() geneexpression
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 60
1
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4
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3.2k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 7.8 years ago by 21k • written 7.8 years ago by ▴ 10
3
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1
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2.8k
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Processing several GSM from GEO database using Barcode and fRMA
frma barcode geneexpression gsm ncbi geo
updated 8.2 years ago by ▴ 830 • written 8.2 years ago by • 0
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4
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2.4k
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ddCT Package for StepOnePlus qPCR output
qPCR ddCt geneexpression
updated 8.5 years ago by ▴ 120 • written 8.5 years ago by ▴ 60
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3
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1.7k
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General suggestions regarding gene expression
geneexpression
updated 8.9 years ago by 53k • written 8.9 years ago by • 0
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0
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1.2k
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Where or how to find the gene interaction with itself?
microarray gene interaction geneexpression
9.1 years ago shaheryar • 0
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1.5k
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Error in SAMseq analysis with R
r samseq microarray rnaseq geneexpression
9.4 years ago namilio • 0
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0
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1.6k
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Methylation and gene expression
methylation geneexpression
9.4 years ago Asma rabe ▴ 290
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2
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1.5k
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Methylation and gene expression data
methylation geneexpression
updated 9.7 years ago by ▴ 130 • written 9.7 years ago by ▴ 290
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3
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2.0k
views
error in drawing MDS plot for eset
MDSplot geneexpression insilicomerging
updated 9.8 years ago by 68k • written 9.8 years ago by ▴ 20
1
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6
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2.4k
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how to deal the effect of enormous gene expression?
deseq2 rnaseq tomato geneexpression
updated 9.9 years ago by 43k • written 9.9 years ago by • 0
0
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1
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1.6k
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Error in MetaQC R package.
r metaqc microarray geneexpression
10.1 years ago Agaz Hussain Wani ▴ 260
0
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3
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2.7k
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problem with WGCNA
geneexpression
updated 10.2 years ago by ★ 3.0k • written 10.2 years ago by • 0
2
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5
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2.3k
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heatmap in R
r language microarray geneexpression
updated 10.4 years ago by ★ 1.1k • written 10.4 years ago by • 0
1
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1
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1.5k
views
gene expression data analysis
microarray geneexpression
updated 10.4 years ago by 68k • written 10.4 years ago by • 0
1
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1
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6.0k
views
NA p and p adjusted value
geneexpression
updated 10.4 years ago by ★ 3.0k • written 10.4 years ago by • 0
1
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2
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7.3k
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explanation of makeContrasts function of limma package
limma microarray R geneexpression
updated 10.5 years ago by ★ 29k • written 10.5 years ago by ▴ 10
56 results • Page 1 of 2
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
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