Showing : Gene expression • reset
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WGCNA: Different Detect Cut Heights Across Multiple Blocks
wgcna clustering gene expression
updated 7.1 years ago by ★ 3.0k • written 7.1 years ago by ▴ 10
2
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1
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4.7k
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Using DESeq2 to analyse TCGA data
deseq2 tcga tcgabiolinks gene expression differential expression
updated 6.2 years ago by 42k • written 6.2 years ago by • 0
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4
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4.6k
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WGCNA: intrepreting grey unassigned "module"?
WGCNA rnaseq gene expression co-expression network
updated 6.1 years ago by ★ 3.0k • written 6.1 years ago by ▴ 10
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2
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barplot with ggplot2 for gene expression
ggplot2 barplot gene expression gene expression
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 130
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11
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2.4k
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Filtering Gene Symbols and Sample Description from GSE files of GEO
gene expression geoquery GSE bioconductor microarray
updated 5.7 years ago by 21k • written 5.7 years ago by ▴ 20
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3
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Reading Illumina HT12 V4.0 Data from GEO into Lumi
lumi geoquery geo illumina human ht-12 v4 gene expression
updated 6.5 years ago by 50k • written 6.5 years ago by • 0
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Test whether expression levels of two gene sets are significantly different
R DESeq2 gene set testing gene expression
7.5 years ago Jon Bråte ▴ 250
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5
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1.9k
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Getting opposite log2 fold change
deseq2 gene expression log2foldchange R
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
3
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3
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1.8k
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Differential Expression Analysis in edgeR using Anova
edger anova gene expression Dispersion
updated 4.9 years ago by • 0 • written 5.3 years ago by • 0
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3
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1.8k
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Algorithm for between and within microarray normalisation (for meta-analysis).
microarray meta-analysis gene expression
updated 5.3 years ago by 0 • written 7.8 years ago by ▴ 70
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6
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1.8k
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Representative gene expression value in one condition with several replicates
rnaseq gene expression edger
updated 6.4 years ago by 50k • written 6.4 years ago by • 0
0
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2
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1.7k
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How can I compare the expression of two genes within the same sample?
gene expression rnaseq deseq2
updated 5.3 years ago by ▴ 30 • written 5.3 years ago by • 0
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3
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1.7k
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RPM data analysis with DESeq2
deseq2 RPM gene expression
5.1 years ago ruhollah.mb • 0
2
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2
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1.4k
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SAM/siggenes: Differential gene expression analysis
SAM siggenes microarray gene expression sam
7.3 years ago Brian Smith ▴ 120
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3
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1.4k
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Anova test on gene expression data
Anova gene expression
updated 6.5 years ago by 65k • written 6.5 years ago by • 0
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4
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1.3k
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Gene clusters based on gene expression across samples
kmeans gene expression clustering
6.6 years ago • updated 6.5 years ago Jane Merlevede ▴ 90
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4
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1.3k
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limma. After running a differential expression analysis... Can you get the individual gene expression levels between individual contrasts for each of…
limma gene expression differential gene expression
6.5 years ago arfranco ▴ 130
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What is the recommended method for running WGCNA on large metatranscriptomic dataset?
wgcna transcriptome big data metagenomics gene expression
6.2 years ago jol.espinoz ▴ 40
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7
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1.3k
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How to read Illumina data used in the MACQ project (GSE5350)
microarray normalization Illumina data MACQ project gene expression
updated 5.0 years ago by 50k • written 5.0 years ago by • 0
0
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3
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1.2k
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How to regress phenotype ~ gene + covars in limma?
limma gene expression microarray R
updated 5.1 years ago by 50k • written 5.1 years ago by • 0
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2
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1.2k
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Help needed to identify common genes among datasets
datasets genes gene expression
updated 8.7 years ago by ★ 13k • written 8.7 years ago by • 0
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0
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Interpreting Affymetrix Human Genome U133 Plus 2.0 samples
gene expression gene expression data cel affy affymatrix
6.3 years ago torgeirous • 0
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1.1k
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Bach effect and PEER/RUV correction on large population
methylation gene expression sva batch effect ruv
7.4 years ago carleshf ▴ 10
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4
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1.1k
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GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 4.3 years ago by ▴ 350 • written 4.3 years ago by • 0
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2
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1.0k
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DESeq2 # of up-and down-regulated genes are approximately equal
deseq2 gene expression
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
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2
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1.0k
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Question about Illuminaio
illuminaio illumina human ht-12 v4 gene expression micorarray
updated 6.1 years ago by ★ 6.5k • written 6.1 years ago by • 0
2
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1
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1.0k
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gene expression data analysis and batch effect methods
batch effect gene expression
updated 6.9 years ago by ▴ 420 • written 7.0 years ago by • 0
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0
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991
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gene expression data analysis and batch effect methods
batch effect gene expression
7.0 years ago tati6406 • 0
3
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4
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982
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edgeR analysis of cells treated with either drug1, drug2, or a time matched control at two different time points, did I set this up correctly?
edger rnaseq gene expression bioinformatics
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
2
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3
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968
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How to calculate overlap between transposable elements differentially expressed in one experiment, with those expressed in another set of samples?
gene expression enrichment RNA-seq DESeq2
updated 5.3 years ago by 42k • written 5.3 years ago by ▴ 30
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899
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Job: Postdoctoral Research Fellowship- reinforcement learning in biology- London
job bioinformatician job machine learning gene expression experimental design Job
5.6 years ago dezer ▴ 10
0
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2
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876
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NanoStringDiff correction for variation between patient
NanoStringDiff GLM Gene expression
updated 4.7 years ago by 65k • written 4.7 years ago by • 0
1
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0
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868
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Job: Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics gene expression time series plant biology circadian Job
4.6 years ago dezer ▴ 10
0
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0
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866
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Normalisation of Data before loading in TMixClust
rna-seq tmixclust k-means clustering gene expression genesis
4.4 years ago astridite • 0
0
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2
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836
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Is there any bioc tool to predict/quantify transcription factor activation using gene expression data?
transcription factor tf activation gene regulatory network gene expression
updated 7.4 years ago by • 0 • written 7.4 years ago by • 0
2
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2
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835
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Limma design matrix separate channel analysis with same control
limma design matrix gene expression
updated 5.3 years ago by 50k • written 5.3 years ago by • 0
0
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1
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748
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Obtaining gene expression value for a list of genes
gene expression
updated 5.7 years ago by 50k • written 5.7 years ago by ▴ 20
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689
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problem with DeMAND, gene expression matrix input
DeMAND gene expression
5.5 years ago chipolino • 0
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2
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645
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Microarray Analysis of Sleep Deprivation Data Experimental Design
limma gene expression r diffeential expression microarray analysis
updated 5.2 years ago by 65k • written 5.2 years ago by • 0
39 results • Page 1 of 1
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Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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