Posts In Category Transcriptomics

Differential Producibility Analysis (DPA) of transcriptomic data to help understand metabolic status of a cell or microorganism

on June 21, 2011 by Bhushan Bonde in Metabolic modelling, Statistics, Systems Biology, Transcriptomics, Tutorials, Comments (2)

Bhushan Bonde Introduction While a vast amount of microarray data is now available freely at the various repositories at NCBI (GEO database) and EBI (ArrayExpress), there is currently no […]

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Volcano plots of microarray data

on by Colin Gillespie in Transcriptomics, Tutorials, Comments (9)

To run the R commands in this post, you should first work through Analysing microarry data in BioConductor. A volcano plot is a scatter plot that is often used when […]

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Gene Set Enrichment Analysis

on June 20, 2011 by Simon Cockell in Transcriptomics, Comments (4)

Introduction The enrichment analysis explored in the previous article can be powerful provided the mechanism used for identifying candidate genes finds all of the genes that are interesting in […]

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Downstream functional analysis of an ‘omics experiment using freely available tools

on by Simon Cockell in Transcriptomics, Comments (4)

Introduction The direct analysis of data from ‘omics experiments (transcriptomics and proteomics especially), focusses on producing lists of genes or proteins of interest (i.e. those that vary in expression, […]

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Analysing microarray data in BioConductor: figures and code

on by Daniel Swan in Transcriptomics, Tutorials, Comments (2)

From the previous article on “Analysing microarray data in BioConductor” the complete code listing is below. Please ensure you have your phenodata.txt file in the right directory to start […]

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Analysing microarray data in BioConductor

on by Daniel Swan in Transcriptomics, Tutorials, Comments (29)

Introduction Microarray analysis is a complex procedure, and using R and the associated BioConductor packages can be a daunting task. In this tutorial we are going to show you […]

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