[BioC] getting started
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?
More information about the Bioconductor