Showing : GeneExpression • reset
9
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7
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9.3k
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DESeq2 timecourse - How to set the experimental design
deseq2 geneexpression timecourse
updated 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 10
5
votes
18
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2.9k
views
DESeq2 comparison two cell types and two genotypes
GeneExpressionWorkflow DESeq2 GeneExpression
updated 3.0 years ago by 41k • written 3.0 years ago by • 0
4
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2
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4.0k
views
Selecting genes based on expressional variance
geneexpression wgcna rnaseq
updated 9.6 years ago by 1.6k • written 9.6 years ago by ▴ 250
3
votes
5
replies
8.5k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 9.5 years ago by ★ 13k • written 9.5 years ago by ▴ 10
3
votes
1
reply
1.7k
views
Processing several GSM from GEO database using Barcode and fRMA
frma barcode geneexpression gsm ncbi geo
updated 6.5 years ago by ▴ 830 • written 6.5 years ago by • 0
2
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3
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1.6k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
2
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5
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1.7k
views
heatmap in R
r language microarray geneexpression
updated 8.7 years ago by ★ 1.0k • written 8.7 years ago by • 0
2
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2
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406
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
2
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2
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6.8k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 2.6 years ago by ★ 4.1k • written 2.6 years ago by ▴ 10
2
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2
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1.6k
views
DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
2.9 years ago SUMIT • 0
2
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5
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11k
views
Calculating FPKM from raw counts data using fpkm() in deseq2
deseq2 r fpkm() geneexpression
updated 5.6 years ago by 41k • written 5.6 years ago by ▴ 60
2
votes
2
replies
821
views
Could use some advice on analyzing ranks of expressed genes in two conditions,
GeneExpression DESeq2 ExpressionData
updated 2.1 years ago by • 0 • written 2.2 years ago by ▴ 10
2
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4
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1.7k
views
Comparing different method for DESEQ2
DESeq2 GeneExpression
updated 19 months ago by 41k • written 19 months ago by • 0
2
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3
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452
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression Clustering ctsGE
9 weeks ago jbgnielson • 0
1
vote
6
replies
1.8k
views
how to deal the effect of enormous gene expression?
deseq2 rnaseq tomato geneexpression
updated 8.2 years ago by 41k • written 8.2 years ago by • 0
1
vote
2
replies
5.7k
views
explanation of makeContrasts function of limma package
limma microarray R geneexpression
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 10
1
vote
1
reply
5.1k
views
NA p and p adjusted value
geneexpression
updated 8.7 years ago by ★ 3.0k • written 8.7 years ago by • 0
1
vote
1
reply
1.2k
views
gene expression data analysis
microarray geneexpression
updated 8.7 years ago by 65k • written 8.7 years ago by • 0
1
vote
3
replies
1.2k
views
General suggestions regarding gene expression
geneexpression
updated 7.2 years ago by 50k • written 7.2 years ago by • 0
1
vote
4
replies
1.8k
views
ddCT Package for StepOnePlus qPCR output
qPCR ddCt geneexpression
updated 6.8 years ago by ▴ 120 • written 6.8 years ago by ▴ 60
1
vote
4
replies
2.0k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 6.1 years ago by 21k • written 6.1 years ago by ▴ 10
1
vote
3
replies
967
views
Troubles implementing LIMMA for paired samples (before/after treatment) comparaisons
GeneExpression R limma MultipleComparison
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
1
vote
1
reply
732
views
Accounting for fish body mass in DE?
GeneExpression edgeR
updated 3.3 years ago by 65k • written 3.3 years ago by • 0
1
vote
3
replies
967
views
DESeq analysis with Biological replicate.
DESeq2 ExpressionData GeneExpression
updated 3.3 years ago by 41k • written 3.3 years ago by • 0
1
vote
1
reply
769
views
Error while using champ.SVD function
GeneExpression
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
1
vote
0
replies
572
views
Error while running Case study n. 3: Integration of methylation and expression for ACC
geneexpression methylation
22 months ago hlee ▴ 10
0
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1
reply
538
views
Error "DESeqDataSetFromMatrix" function not found
GeneExpression
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
0
votes
3
replies
11k
views
How to combine expression values of multiple probes for one gene
probe convert geneexpression onechannelgui
updated 8.8 years ago by ▴ 830 • written 8.8 years ago by ▴ 10
0
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3
replies
997
views
CountOverlap
GeneExpression ChIPSeqData
updated 19 months ago by 65k • written 19 months ago by ▴ 20
0
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2
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2.0k
views
Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
2.6 years ago p.l.chen • 0
0
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0
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443
views
Free Gibbson energy RNA doublex
GeneExpression RNAinteract
20 months ago Tamina • 0
0
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1
reply
2.4k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
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2
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931
views
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 22 months ago by ★ 1.3k • written 22 months ago by • 0
0
votes
1
reply
476
views
Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
9 months ago Arianna • 0
0
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0
replies
1.2k
views
Methylation and gene expression
methylation geneexpression
7.7 years ago Asma rabe ▴ 290
0
votes
2
replies
1.1k
views
Methylation and gene expression data
methylation geneexpression
updated 8.0 years ago by ▴ 130 • written 8.0 years ago by ▴ 290
0
votes
1
reply
1.9k
views
GDCprepare of STAR - counts
GeneExpression TCGAbiolinks
updated 19 months ago by • 0 • written 2.0 years ago by • 0
0
votes
1
reply
634
views
Aggregate differentially expressed genes across all contrast results using DEVis
DifferentialExpression NanoporeRNASeq DESeq2 GeneExpression DEVis
updated 23 months ago by 65k • written 23 months ago by • 0
0
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0
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1.1k
views
Using segAnglePo() for a set of genes
geneexpression genesetenrichment segAnglePo
9.4 years ago Peter.Wood • 0
0
votes
3
replies
1.6k
views
error in drawing MDS plot for eset
MDSplot geneexpression insilicomerging
updated 8.1 years ago by 65k • written 8.1 years ago by ▴ 20
0
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0
replies
846
views
Volcano plot: Putting calculated values in legend
GeneExpression
updated 2.1 years ago by ★ 3.9k • written 2.1 years ago by • 0
0
votes
0
replies
1.5k
views
easyRNASeq: Number of total counts
GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt
10.1 years ago Guest User ★ 13k
0
votes
1
reply
629
views
Heatmap of two conditions from the normalized gene count data
GeneExpression heatmaps
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
1
reply
1.3k
views
Error in MetaQC R package.
r metaqc microarray geneexpression
8.4 years ago Agaz Hussain Wani ▴ 260
0
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3
replies
1.8k
views
problem with WGCNA
geneexpression
updated 8.5 years ago by ★ 3.0k • written 8.5 years ago by • 0
0
votes
0
replies
900
views
Where or how to find the gene interaction with itself?
microarray gene interaction geneexpression
7.4 years ago shaheryar • 0
0
votes
2
replies
1.7k
views
FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
12 months ago CDSPARKS ▴ 10
0
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0
replies
1.2k
views
Error in SAMseq analysis with R
r samseq microarray rnaseq geneexpression
7.7 years ago namilio • 0
0
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0
replies
619
views
Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
3.5 years ago coobzie • 0
0
votes
2
replies
961
views
Gene expression in R
limma edgeR Biobase GeneExpression
2.7 years ago • updated 2.6 years ago sogol.bouyeh • 0
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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