[BioC] How to get started with bioconductor ?

[Robert Gentleman]

On Wed, Sep 10, 2003 at 03:12:24PM +0100, michael watson (IAH-C) wrote:
> Luke
> 
> 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...)
> 
 Not heresy, there is lots of good software that is not in
 Bioconductor, but I'm not entirely sure why you want to ignore the
 stuff that is in it - there are several options there, including
 simple basic built in R functions, limma and hopefully some new
 offerings in the next few weeks.

 It is good to look around at what is available, but one shouldn't
 miss what is under one's nose either.

  Robert


> Mick
> 
> -----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 ?
> 
> 
> 
> Hello,
> 
> 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 ?
> 
> Thanks,
> 
> Luke Whitaker
> Inpharmatica
> 
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-- 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
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