[BioC] getting started

Gordon Smyth smyth at wehi.edu.au
Thu Mar 11 01:33:45 MET 2004

At 10:50 AM 11/03/2004, Dennis Hazelett wrote:
>I have been playing around with bioconductor for a few days now, trying to 
>normalize data I have from genepix software. No one at my institution uses 
>Bioconductor for microarray analysis (in fact, to my knowledge, they don't 
>do any normalization beyond using a reference sample for one of the 
>channels) so there is little help here. I have successfully been able to 
>read in individual files and make nice graphs with them using marrayPlots, 
>but ultimately I would like to be able to do loess, scale normalization 
>between slides, and finally some sort of bayesian analysis for 
>differential expression. Right now I'm stuck on reading in my data using 
>marrayInput. But I don't even know that marrayInput is the best 
>package--should I be using limma?

For the processes you describe, you can use either limma or 
marrayInput/marrayNorm. It's just a matter of what style you prefer. Maybe 
have a look at one more document, the limma User's Guide.

A little later down the track you might want to use limma for differential 
expression. At any stage, you can apply as.MAList() to your marray object 
and you're away.


>  I've read oh i don't know--3, 4 vignettes?-- that each have some help on 
> the subject of reading in data, but they use a data set--"swirl"--am I 
> mistaken here or is swirl composed of 4 sets of microarray files that 
> *have already been read in*? The widget doesn't help. Should objects like 
> swirl correspond to treatment groups? Where in marrayInfo does one put 
> information about the target sample? How does that get related back to 
> actual array data? There's a lot of documentation on what the classes 
> are, but not on how to use them. I don't expect answers to these 
> questions--I've scoured vignettes and message boards for this type of 
> info. I just want to know, can anyone point me in the right direction?

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