[BioC] alt cdf env probe index config problem

[Rhonda DeCook]

I attempted to submit this post as a non-member last week, but it never 
appeared on the list.  I'm re-posting as a member now, hope it isn't a 
duplicate...

I'm using the 'altcdfenv' package to create an alternative CDF environment for 
the "ATH1-121501" chip.  We would like to re-do our analysis on 30 chips after 
removing about 15,000 probes.  I'm first trying to succeed at creating a new 
CDF env by removing whole genes (or probe sets) from the analysis.  It looks 
like I'm close(my new environment has the correct number of subsetted genes), 
but when I request the probe indices for a given gene using the new CDF 
environment 'env.ath.new.cdf' and the 'get' function, the information is 
returned as a list of length 22, instead of an 11x2 matrix as in the original 
CDF environment.  

> get(ls(env.ath.new.cdf)[1],env.ath.new.cdf) 
$"244901_at"
 [1] 501131 251604 261891 230387 217334 451116 488419 215764  92381 334408  
53876 501843 252316 262603 231099 218046
[17] 451828 489131 216476  93093 335120  54588

## Using the original CDF environment:
> get(ls(ath1121501cdf)[1],ath1121501cdf)
          pm     mm
 [1,] 501131 501843
 [2,] 251604 252316
 [3,] 261891 262603
 [4,] 230387 231099
 [5,] 217334 218046
 [6,] 451116 451828
 [7,] 488419 489131
 [8,] 215764 216476
 [9,]  92381  93093
[10,] 334408 335120
[11,]  53876  54588

This shape difference makes the suite of affy tools incompatible for the new 
CDF environment.  



I've followed the vignette for 'alternative CDF environments' and I've looked 
around the R-list, but I'm not sure where to go next. Somehow I've got to get 
the new CDF environment to see this list as a matrix or I'll end up with errors 
like:

> indexProbes(cel.files.30.lines, which="pm", genenames="244901_at")[[1]]
Error in ans[[i]][, i.probes] : incorrect number of dimensions


Any suggestions?

Thanks,
Rhonda

P.S. I've included the code for the creation of 'env.ath.new.cdf' below.




_______________________________________________________________
R version 2.0.1
altcdfenv version 1.1-10

> ## Create an alternative CDF environment:
> ath.old.cdf<-wrapCdfEnvAffy(ath1121501cdf,712,712,"ath1121501cdf")
> ids<-geneNames(ath.old.cdf)  
> ids.subset<-ids[c(1,2,3)]    
> ath.new.cdf<-ath.old.cdf[ids.subset] 
> print(ath.new.cdf)
>
Instance of class CdfEnvAffy:
 name     : ath1121501cdf-subset 
 chip-type: ath1121501cdf 
 size     : 712 x 712 
 3 probe set(s) defined.
>
> env.ath.new.cdf<-as(ath.new.cdf,"environment") 
>
>
>
> ## Load in the 30 cel files:
> setwd("D:/Rhonda/Lall/2nd_experiment/cel_files")
> cel.files.30.lines<-ReadAffy()           
>
> ## Re-assign the cdf environment for the AffyBatch:
> cel.files.30.lines at cdfName<-"env.ath.new.cdf"
>
> gn.new<-geneNames(cel.files.30.lines)
> gn.new
[1] "244901_at" "244902_at" "244903_at"
> ls(env.ath.new.cdf)  
[1] "244901_at" "244902_at" "244903_at"