January 2010
Beginner
634 pages
19h 50m
English
Content preview from R in a Nutshell
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.
Key Bioconductor Packages
The Bioconductor repository contains over 300 packages for working with genetic data. Below is a list of some popular packages, with short descriptions of the classes and functions that they contain.
| Category | Package | Description |
|---|---|---|
| Loading, preprocessing | aCGH | Classes and functions for array comparative genomic hybridization data. Functions for reading aCGH data from image analysis output files and clone information files and for creating aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing, and plotting aCGH objects. |
| affy | Methods for Affymetrix oligonucleotide arrays. Includes class definitions for representing microarray data. Also includes methods for importing data, quality control, and normalization. | |
| affyQCReport | A package to generate QC reports for Affymetrix array data. | |
| arrayQuality | Functions for performing print-run and array-level quality assessment. | |
| gcrma | Background adjustment using sequence information. The
main function gcrma
converts background-adjusted probe intensities to expression
measures using the same normalization and summarization
methods as RMA (robust multiarray average). | |
| limma | Limma is an R package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | |
| lumi | Functions to preprocess Illumina microarray (BeadArray) data. It includes functions of Illumina data input, quality control, variance stabilization, ... |
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
and much more.
Read now
Unlock full access
More than 5,000 organizations count on O’Reilly
O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.Julian F.
I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.