[BioC] getting started

[Jean Yee Hwa Yang]

Hi Dennis,

Put all you gpr files and the gal file in the same directory.  
Set your working directory to where your data is. The type:

library(marrayTools)
library(marrayPlots)
data <- gpTools(raw=TRUE)
data at maGb <- data at maRb <- matrix(0,0,0)
datanorm <- maNorm(data)
write.xls(maM(datanorm), file="results.xls")

The above 6 lines will perfrom all diagnostic plots, do the normalization
and output the results.  If you don't need diagnostic plots, just try

library(marrayTools)
gpTools(bg=FALSE, quality=FALSE, plot=FALSE)

and it will out put the normalized data for you in the same directory.

Cheers

Jean
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Jean Yee Hwa Yang			 jean at biostat.ucsf.edu
 Lung Biology Center, 		           Tel: (415) 476-3368
 University of California,		   Fax: (415) 476-6014
 500 Parnassus Avenue, MU 420-W,  San Francisco, CA 94143-0560
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Wed, 10 Mar 2004, 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 
> 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 
> 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
> 
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