[BioC] How to get started with bioconductor ?

Luke Whitaker luke at inpharmatica.co.uk
Wed Sep 10 11:25:56 MEST 2003


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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