Showing : geneexpression • reset
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
1 day ago Reuben • 0
2
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1
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220
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Using Affymetrix Custom Array
ArrayExpress makecdfenv AffymetrixChip gcrma GeneExpression
updated 9 weeks ago by 67k • written 9 weeks ago by • 0
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256
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
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9
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858
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
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3
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760
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"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
10 months ago jbgnielson • 0
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731
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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
14 months ago Manthos • 0
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3
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 16 months ago by 52k • written 16 months ago by • 0
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1
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780
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
18 months ago Arianna • 0
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2
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2.9k
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FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
21 months ago CDSPARKS ▴ 30
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903
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Heatmap of two conditions from the normalized gene count data
GeneExpression heatmaps
updated 22 months ago by ★ 4.6k • written 22 months ago by • 0
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1
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3.8k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 23 months ago by ★ 4.6k • written 23 months ago by • 0
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4
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2.2k
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Comparing different method for DESEQ2
DESeq2 GeneExpression
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
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3
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1.4k
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CountOverlap
GeneExpression ChIPSeqData
updated 2.3 years ago by 67k • written 2.3 years ago by ▴ 20
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595
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Free Gibbson energy RNA doublex
GeneExpression RNAinteract
2.4 years ago Tamina • 0
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0
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782
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Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
2.5 years ago hlee ▴ 10
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1.2k
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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 2.5 years ago by ★ 1.4k • written 2.5 years ago by • 0
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1
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763
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Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 0
0
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1
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850
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Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 2.6 years ago by 67k • written 2.6 years ago by • 0
1
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1
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1.0k
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Error while using champ.SVD function
GeneExpression
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
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1
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2.2k
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GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 2.3 years ago by • 0 • written 2.7 years ago by • 0
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0
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1.1k
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Volcano plot: Putting calculated values in legend
GeneExpression
updated 2.8 years ago by ★ 4.0k • written 2.8 years ago by • 0
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2
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1.0k
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Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 2.8 years ago by • 0 • written 2.9 years ago by ▴ 10
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2
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2.5k
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
3.3 years ago p.l.chen • 0
2
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2
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7.8k
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Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 3.3 years ago by ★ 4.6k • written 3.3 years ago by ▴ 10
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2
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1.3k
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Gene expression in R
limma edgeR Biobase GeneExpression
3.4 years ago sogol.bouyeh • 0
2
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2
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2.0k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.6 years ago SUMIT • 0
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18
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3.5k
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DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow DESeq2 GeneExpression
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
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3
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1.2k
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DESeq analysis with Biological replicate.
DESeq2 ExpressionData GeneExpression
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
1
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1
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867
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Accounting for fish body mass in DE?
GeneExpression edgeR
updated 4.0 years ago by 67k • written 4.0 years ago by • 0
0
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1
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886
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Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 4.1 years ago by ▴ 510 • written 4.1 years ago by • 0
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3
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1.2k
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Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression R limma MultipleComparison
updated 4.1 years ago by 67k • written 4.1 years ago by • 0
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764
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
4.2 years ago coobzie • 0
2
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5
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13k
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Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2 r fpkm() geneexpression
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 60
1
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4
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2.4k
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Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 6.8 years ago by 21k • written 6.8 years ago by ▴ 10
3
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1
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2.0k
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Processing several GSM from GEO database using Barcode and fRMA
frma barcode geneexpression gsm ncbi geo
updated 7.2 years ago by ▴ 830 • written 7.2 years ago by • 0
1
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4
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2.1k
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ddCT Package for StepOnePlus qPCR output
qPCR ddCt geneexpression
updated 7.5 years ago by ▴ 120 • written 7.5 years ago by ▴ 60
1
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3
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1.4k
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General suggestions regarding gene expression
geneexpression
updated 7.9 years ago by 52k • written 7.9 years ago by • 0
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0
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1.1k
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Where or how to find the gene interaction with itself?
microarray gene interaction geneexpression
8.1 years ago shaheryar • 0
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1.3k
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Error in SAMseq analysis with R
r samseq microarray rnaseq geneexpression
8.4 years ago namilio • 0
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0
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1.4k
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Methylation and gene expression
methylation geneexpression
8.4 years ago Asma rabe ▴ 290
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2
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1.3k
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Methylation and gene expression data
methylation geneexpression
updated 8.7 years ago by ▴ 130 • written 8.7 years ago by ▴ 290
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3
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1.8k
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error in drawing MDS plot for eset
MDSplot geneexpression insilicomerging
updated 8.8 years ago by 67k • written 8.8 years ago by ▴ 20
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6
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2.1k
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how to deal the effect of enormous gene expression?
deseq2 rnaseq tomato geneexpression
updated 8.9 years ago by 43k • written 8.9 years ago by • 0
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1
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1.4k
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Error in MetaQC R package.
r metaqc microarray geneexpression
9.1 years ago Agaz Hussain Wani ▴ 260
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3
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2.2k
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problem with WGCNA
geneexpression
updated 9.2 years ago by ★ 3.0k • written 9.2 years ago by • 0
2
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5
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1.9k
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heatmap in R
r language microarray geneexpression
updated 9.4 years ago by ★ 1.0k • written 9.4 years ago by • 0
1
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1
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1.3k
views
gene expression data analysis
microarray geneexpression
updated 9.4 years ago by 67k • written 9.4 years ago by • 0
1
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1
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5.4k
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NA p and p adjusted value
geneexpression
updated 9.5 years ago by ★ 3.0k • written 9.5 years ago by • 0
1
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2
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6.4k
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explanation of makeContrasts function of limma package
limma microarray R geneexpression
updated 9.5 years ago by ★ 28k • written 9.5 years ago by ▴ 10
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3
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12k
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How to combine expression values of multiple probes for one gene
probe convert geneexpression onechannelgui
updated 9.5 years ago by ▴ 840 • written 9.5 years ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by QN ▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Comment: EdgeR Biological CVs by ATpoint ★ 4.6k
"Joseph" is a spam bot...
Answer: How to sort negative log2FC or FC in RNAseq for GSEA? by ATpoint ★ 4.6k
GSEA asks whether there are general shifts in gene expression towards certain terms. Hence, you would not split your results tables but ord…
Comment: EdgeR Biological CVs by James • 0
Thank you Gordon and Joseph. I presume question (1) would be answered by using a prior G0 of 0? For question (2), I was expecting a biolog…
Comment: EdgeR Biological CVs by Joseph ▴ 10
I believe the published study provides answers to your questions. Yunshun Chen and Pedro Baldoni's recent papers on edgeR may also be of in…
Votes
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Comment: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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