[BioC] Which application to start BioConductor?

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Jan 6 23:11:53 CET 2010


On Wed, Jan 6, 2010 at 4:35 PM, cihan inan <cihan253 at gmail.com> wrote:
> Well I am a biology student at university. and next year I will be a master
> student. I am planning to be in bioinformatics department. that's why I need
> to learn as much as I can. But at first I want to learn analysis about
> microarrays. from beginning to the end.  normalisation etc... I have 6
> months and I think it is enough to learn a lot of think about microarrays.

No simple answer, but try this after installing Bioconductor.

R> library(affy)
R> openVignette()

Select the 1st one (eg. the primer).

It deals with getting your feet wet w/ affy arrays (some
normalization/quality control stuff, too). Check out the papers in the
References section too for more info.

As you get going, you'll quickly find the need to use limma as well: a
package to call differentially expressed genes between samples. It's a
very flexible, which is great, but also a bit complex since it's so

Load the library and fire up its user's guide

R> library(limma)
R> limmaUsersGuide()

Lots of good references in its Bibliography.

6 months is *just about* enough time to get through that user guide
plus refs (and their refs) + getting comfortable w/ R and Bioconductor
... you might find you'd like even more time, though ... let us now

Good luck,


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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