Lately I've been using the limma package often for analyzing microarray data. When I read in Affy CEL files using ReadAffy(), the resulting ExpressionSet won't contain any featureData annotation. Consequentially, when I run topTable to get a list of di...
I just got this announcement from EMBL-EBI about an RNA-seq/ChIP-seq analysis hands-on course. Find the full details, schedule, and speaker list here.Title: Advanced RNA-Seq and Chip-Seq Data Analysis Course Date: May 1-4 2012 Venue: EMBL-EBI, Hinxton,...
I found the slides below on the education page from Bioinformatics & Research Computing at the Whitehead Institute. The first set (PDF) gives an overview of the methods and software available for quality assessment of microarray and RNA-seq experim...
Just a brief selection of items that caught my eye this week. Note that this is a Friday as opposed to Friday, lest you mistake this for a new, regular feature. 1. R/statistics ggbio A new Bioconductor package which builds on the excellent ggplot graphics library, for the visualization of biological data. R development...
Gene Expression Omnibus is NCBI's repository for publicly available gene expression data with thousands of datasets having over 600,000 samples with array or sequencing data. You can download data from GEO using FTP, or download and load the data direc...
In general, the standard practice for correcting for population stratification in genetic studies is to use principal components analysis (PCA) to categorize samples along different ethnic axes. Price et al. published on this in 20...
I just accepted an offer for a faculty position at the University of Virginia in the Center for Public Health Genomics / Department of Public Health Sciences. Starting in October I will be developing and directing a new centralized bioinformatics core ...
In an ideal world, all bioinformatics tools would be made available via the Web as a web service with an API, as well as a standalone package to download for local use. This is rarely the case and sometimes, even where one or the other is available, factors such as cost come into play....
Which topics are the most popular at the BioStar bioinformatics Q&A site? One source of data is the tags used for questions. Tags are somewhat arbitrary of course, but fortunately BioStar has quite an active community, so “bad” tags are usually edited to improve them. Hint: if your question is “How to find SNPs”,...
Lately, I've been using statistical tests on a daily basis. I've noticed that I have to format my data the same way in order to get it into R (tab-delimited flat file essentially). Every other change in order to prep that data structure for any sort of...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).