R help - Oct 2011 - Creating One Single Object Linking Multiple Datapoints

Thanks, Martin.  Based on my previous post, I thought of a more general
formulation of my question  that I think would be helpful to ask here.
What's the best way to build an R object that links multiple datapoints
about different people?  I mean, I happen to have datasets that have
individual gene expression data tied to individual patient characteristics
(how long they survived, age, gender, and other things).  But if I were a
baseball statistician wanting to link individual batting data to individual
baseball player characteristics (age, height, weight, etc), the idea would
be the same, I think.

I could do this in Python but I'm not really sure how it would work in R and
would greatly appreciate any advice about how to implement this.

Thanks!

Ben


On Fri, Oct 7, 2011 at 10:50 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:
> Hey Ben -- this is a bioconductor question so please ask on the
> Bioconductor mailing list. Good news, you don't have to subscribe to
post
>
>
http://bioconductor.org/help/**mailing-list/<http://bioconductor.org/help/mailing-list/>
>
> Martin
>
>
> On 10/07/2011 07:27 AM, Ben Ganzfried wrote:
>
>> Hey,
>>
>> I have code that can check the quality of a data set we're working
with
>> (expression data), and I'm having some trouble writing code that
would
>> make
>> the expression data we have tie to other data we want to link it to
>> (called
>> phenotype data).  Does anyone have any advice on how I could make a
single
>> object that would do this?  Other relevant info: I want to use the
pdata()
>> function, and I have all the phenotype data available as csv files. 
Here
>> is
>> what I have in regards to the expression data:
>>
>> library(affy)
>> library(arrayQualityMetrics)
>>
>> inputargs<- commandArgs(TRUE)
>> print(inputargs)
>> sessionInfo()
>>
>> strInputAccession<- inputargs[1]
>> strBaseDir<- inputargs[2]
>>
>> processedDir<-
>>
paste(strBaseDir,**strInputAccession,"PROCESSED/**DEFAULT",sep="/")
>> qcDir<-
paste(strBaseDir,**strInputAccession,"QC",sep="/"**)
>> sampleFile<-
>>
paste(processedDir,"/",**strInputAccession,"_**RAWfilenames.txt",sep="")
>> defaultExprs<-
>>
paste(processedDir,"/",**strInputAccession,"_default_**exprs.csv",sep="")
>>
>> if(file.exists(sampleFile)){
>>   affyobj<- try(ReadAffy(filenames=read.**table(sampleFile,as.is
>> =T,header=FALSE)[,1]))
>>   if(class(affyobj)=="try-error"**){
>>     rm(affyobj)
>>   }else{
>>     sampleNames(affyobj)<-
sub("\\..*","",sampleNames(**affyobj))  #get
>> rid
>> of .CEL etc extension, just keep GSM
>>   }
>> }
>>
>> if(!exists("affyobj")){
>>   mdExprs<- as.matrix(read.csv(**defaultExprs,row.names=1))
>>   if( min( mdExprs, na.rm = TRUE )>= 0&  max( mdExprs, na.rm =
TRUE )>= 50
>>
>> ) {
>>     mdExprs<- log(mdExprs, base = 2) }
>>   affyobj<- new("ExpressionSet",exprs=**mdExprs)
>> }
>>
>> x<- arrayQualityMetrics(**expressionset = affyobj,
>>                          outdir=qcDir,
>>                          force = TRUE,
>>                          spatial=FALSE)
>>
>>        [[alternative HTML version deleted]]
>>
>> ______________________________**________________
>> R-help@r-project.org mailing list
>>
https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide http://www.R-project.org/**
>> posting-guide.html <http://www.R-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>
	[[alternative HTML version deleted]]