Showing : geneexpression • reset
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Reading gene expression data in GPR format and converting it to xlsx format
BiocWorkflowTools BiomedicalInformatics GeneExpression
updated 11 months ago by 68k • written 11 months ago by • 0
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1
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738
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WGCNA sample-data preprocessing order
Microarray WGCNA GeneExpression
updated 12 months ago by ★ 5.0k • written 13 months ago by • 0
2
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1
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622
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Using Affymetrix Custom Array
ArrayExpress makecdfenv AffymetrixChip gcrma GeneExpression
updated 15 months ago by 68k • written 15 months ago by • 0
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1
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586
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 15 months ago by 43k • written 15 months ago by • 0
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9
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1.5k
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 21 months ago by ★ 5.0k • written 21 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
23 months ago jbgnielson • 0
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1.2k
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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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5.5k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
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1
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1.4k
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
2.6 years ago Arianna • 0
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2
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4.4k
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FeatureCounts Output Counts at Exon Level Using Default Settings, want gene level
GeneExpression
2.8 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 3.0 years ago by • 0
0
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1
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5.5k
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DESeq2 after Seurat analysis on integrated datasets
DESeq2 SingleCell GeneExpression Seurat
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
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4
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3.3k
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Comparing different method for DESEQ2
DESeq2 GeneExpression
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
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3
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1.8k
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CountOverlap
GeneExpression ChIPSeqData
updated 3.4 years ago by 68k • written 3.4 years ago by ▴ 20
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824
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Free Gibbson energy RNA doublex
GeneExpression RNAinteract
3.5 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
3.6 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 3.6 years ago by ★ 1.4k • written 3.6 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 3.7 years ago by 68k • written 3.7 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 3.8 years ago by ▴ 780 • written 3.8 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 3.4 years ago by • 0 • written 3.8 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 3.9 years ago by • 0 • written 3.9 years ago by ▴ 10
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2
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3.1k
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Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
4.4 years ago p.l.chen • 0
2
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2
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10k
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Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 4.4 years ago by ★ 5.0k • written 4.4 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
2
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2
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2.5k
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DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
4.7 years ago SUMIT • 0
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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 4.8 years ago by 43k • written 4.8 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 5.1 years ago by 43k • written 5.1 years ago by • 0
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1
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1.1k
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Accounting for fish body mass in DE?
GeneExpression edgeR
updated 5.1 years ago by 68k • written 5.1 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 5.2 years ago by ▴ 510 • written 5.2 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 5.2 years ago by 68k • written 5.2 years ago by • 0
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975
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
5.3 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 7.4 years ago by 43k • written 7.4 years ago by ▴ 60
1
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4
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3.3k
views
Need help loading gene expression data into R using either ArrayExpress or GEOquery R packages
arrayexpress geoquery geneexpression
updated 7.9 years ago by 21k • written 7.9 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 8.3 years ago by ▴ 830 • written 8.3 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 8.6 years ago by ▴ 120 • written 8.6 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 9.0 years ago by 53k • written 9.0 years ago by • 0
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1.3k
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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
9.5 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
9.5 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 9.8 years ago by ▴ 130 • written 9.8 years ago by ▴ 290
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3
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2.1k
views
error in drawing MDS plot for eset
MDSplot geneexpression insilicomerging
updated 9.9 years ago by 68k • written 9.9 years ago by ▴ 20
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6
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2.5k
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how to deal the effect of enormous gene expression?
deseq2 rnaseq tomato geneexpression
updated 10.0 years ago by 43k • written 10.0 years ago by • 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
10.2 years ago Agaz Hussain Wani ▴ 260
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3
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2.7k
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problem with WGCNA
geneexpression
updated 10.3 years ago by ★ 3.0k • written 10.3 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 10.5 years ago by ★ 1.1k • written 10.5 years ago by • 0
1
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1
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1.6k
views
gene expression data analysis
microarray geneexpression
updated 10.5 years ago by 68k • written 10.5 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 10.5 years ago by ★ 3.0k • written 10.5 years ago by • 0
1
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2
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7.4k
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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
Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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