[BioC] getting started

[Robert Gentleman]

On Wed, Mar 10, 2004 at 03:50:06PM -0800, Dennis Hazelett wrote:
> Hello,
> 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 


 limma and EBarrays are options for Bayesian analysis.

 Every package is supposed to have one or more vignettes that guide
 you through a basic analysis. You can find these using openVignette
 and you can explore them more thoroughly using the vExplorer function
 just go

  library(tkWidgets)
  vExplorer()


> using marrayInput. But I don't even know that marrayInput is the best 
> package--should I be using limma? 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 

  which widget?

> 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?
> -Dennis

  You should not really need to know about the classes -> they should
  be relatively transparent at the user level. What you should find it
  easy to do is to read in your data and make a simple analysis.

  When I looked at the vignette for marrayInput I found that in
  Section 4 there were specific details for reading data in.
  The example might be a bit confusing - there are two parts to it, in
  one part the data have already been read in, as you identified, but
  the raw data files are also there and it is in Section 4 that the
  specific details are given. You can also find the raw data files 
  by looking in the library directory for R - in marrayInput/data/
  (and they are GenePix data).

 Hope that helps,
   Robert



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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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