In this session we'll discuss the Oligo package.
That is a package for pre-processing and
handling Affymetrix and nimble chimp micro rays.
Specifically gene expression micro rays and snip micro rays.
So Affymetrix chips, so called single column microarrays.
They are widely used, an early success of
the Bioconductor project was to provide
a very good method for pre-processing and
analyzing gene expression erased from Affymetrix.
This package is a continuation or a second version of
an earlier package in Bioconductor called the Affy package.
The Affy package was specifically focused on gene expression,
micro-rays from Affymetrix, and then later on, the authors realized that they could
handle gene expression and snip chips, and also for both Affymetrix and Nimble Jim.
Nimble Jim is another company that makes micro-rays that were later
purchased by Affymetrix, and shall we say for
some applications, in some areas of genomics, there have been,
these arrays have been used a lot but they're not very commonly used.
Let's start off by loading the Oligo packets,
and we're also going to load the AL query packets,
because we're going to get some data from GU in order to normalize.
So, we're going to look at a specific GUID and we want to get so called cell files.
So for Affymetrix, microrays, raw data stored in a binary form,
typically a binary format called cell.
These are not the standard files we get from GU.
These are always submitted as supplementary files from GU.
So the way we get these cell files is we know what the system number
of the experiment is, and then we get the supplementary files.