reformat multiset for ggplot2

[Dr Proteome]

Dear people,
I'm trying to analyse microarray data and I've started using R only a
few months ago. So I've been playing around with several packages but
only recently I found ggplot2 and it looks great and exactly what I
need to visualise my data and results. Sadly I have not been able to
try it on my own data yet.
The problem is this: ( I still feel an R-novice so please forgive me
if my explanation looks a bit unclear)

My data is organised in a muliset (peptide microarray for protein-
binding studies) ,
- the phenoData contains the annotation of the samples that are
applied to the arrays
- the featureData contains all the info of the peptides that are on
the chip (name sequence, concentration, position etc)
- assayData: for each peptide several parameters are available
(signal, background, shape etc)

my problem here is, how to get my data in the right format to be able
to apply ggplot2?

I was looking at the diamonds dataset, annd understand the data
structure.
Basically every peptide on each array I use can be considered as a
single diamond for which phenoData (ID variables) , featureData and
assayData is available.
I have not been able to reformat my multiset into the format as shown
in the diamonds table.

I have been using the reshape package to melt the data frame but was
only partially succesful.

Can you give me some advice on what would be the best way to solve
this problem (if available)?

thanks for the help!
Rene

[Ista Zahn]

An actual reproducible example would help...

-Ista

--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org

[Tim Triche]

you're going to end up reshaping it column-by-column or frame-by-frame, or at least I did.  melt chokes on my data (methylation data mostly, some snps, some expression sets)

ggplot2 doesn't really expect an eSet-derived object to play with.  Although, if you write some hooks so that ggplot2 does play nice with ExpressionSet-like classes, you will be a hero forever.

Anyways, how many peptides do you have?  A ton?  Can you post up some code and a little throwaway eSet-like data file that resembles your own?  I've dealt with this sort of thing in my code, so I am curious how others will approach the same problem.

--
Statisticians, like artists, have a bad habit of falling in love with their models.
--George Box