[BioC] How to save the RMA result in .RData file (oligo package)?

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Nov 11 03:01:25 CET 2009


Hi Peng,

On Nov 10, 2009, at 8:53 PM, Peng Yu wrote:

> On Tue, Nov 10, 2009 at 2:21 PM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
>> Hi,
>>
>> On Nov 10, 2009, at 3:17 PM, Peng Yu wrote:
>>
>>> I currrently use the following code to generate RMA results (in
>>> exprs.txt). But it is inconvenient to save a text file. If I can  
>>> save
>>> the result in '.RData' format, it would be faster.  I'm wondering  
>>> what
>>> variable in 'eset' I should 'save()' into '.RData' format.
>>>
>>> library(oligo)
>>> cel_files = list.celfiles('.', full.names=T,recursive=T)
>>> data=read.celfiles(cel_files)
>>> eset=rma(data)
>>> write.exprs(eset, file="exprs.txt", sep="\t")
>>
>> It shouldn't be different than saving another other R object:
>>
>> save(eset, file="exprs.eset.rda")
>
> 'eset' has a lot of things that I don't need. I only want to save the
> RMA corrected expression values that were in 'exprs.txt' to a '.RData'
> file.

I'd suggest reading some of the introductory vignettes you have access  
to when you load the affy library.

In particular, check out the "Primer", and "An introduction to Biobase  
and ExpressionSets". You'll find it quite helpful down the road if you  
get familiar with working with ExpressionSets, etc. now (it can be a  
pain at first).

So, you'd do:

...
eset <- rma(data)
expr.matrix <- exprs(eset)
save(expr.matrix, file="exprs.rda")
...

HTH,
-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact



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