[BioC] How to get started with bioconductor ?

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Sep 10 16:12:24 MEST 2003


For basic data reading and normalisation functions, look at the marray* and limma classes (they both have very good documentation)
For simple t tests between two conditions, look at multtest
And for ANOVA style models, look outside of Bioconductor at Gary Churchills MAANOVA library (http://www.jax.org/staff/churchill/labsite/software/anova/rmaanova/)  (I know, I know, heresy...)


-----Original Message-----
From: Luke Whitaker [mailto:luke at inpharmatica.co.uk]
Sent: 10 September 2003 10:26
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] How to get started with bioconductor ?


I need to do some straightforward analysis on two-dye microarray
data. I want to be able to estimate fold-regulation for each gene
between two conditions (eg treated/untreated etc).

The first chips I had to analyse had 200 genes and I "rolled
my own" analysis using lm() etc. which seemed to work OK, but I
now have chips with aprox 1,700 genes and the method I was using
(essentially ANOVA with one level of explanatory factor per gene)
now runs out of memory.

I would like to use Bioconductor, but looking at the documentation,
I cannot see the forest for the trees. I have had a look at limma,
and think it may do what I want, but it seems to use quite a
sophisticated bayesian analysis which I do not completely understand,
and I would prefer to start at least with something fairly simple. As
usual, I have much less time than I would like to do this.

Is there one basic bioconductor function for estimating fold
regulation in a two dye experiment ?


Luke Whitaker

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