[BioC] Can't normalize with alternative affy CDF environment

[Ken Termiso]

Hi all,

I went through the excellent tutorial at
http://www.bioconductor.org/repository/devel/vignette/ngenomeschips.pdf  
regarding how to make an alternative CDF environment for affy chips. I'm 
using HG-U133a2 chips. This is R 2.0.1 on OSX 10.3 with all BC libraries 
updated..

Briefly, I did this --

1)made a cdf with a subset of 1,571 probes (out of 22277) that i wanted to 
keep for re-analysis by following the tutorial.

2) saved the cdf

save(m5_CDF, file = "m5_CDF.Rdata")

3) loaded the CDF into a blank workspace.

load(file = "m5_CDF.Rdata")

ls()
[1] "m5_CDF"

str(m5_CDF)
Loading required package: altcdfenvs
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
	 Vignettes contain introductory material.  To view,
	 simply type: openVignette()
	 For details on reading vignettes, see
	 the openVignette help page.
Loading required package: affy
Loading required package: reposTools
Loading required package: matchprobes
Loading required package: hgu95acdf
Loading required package: hgu133aprobe
Loading required package: plasmodiumanophelescdf

Attaching package 'plasmodiumanophelescdf':


	The following object(s) are masked from package:hgu95acdf :

	 i2xy xy2i

Formal class 'CdfEnvAffy' [package "altcdfenvs"] with 8 slots
  ..@ envir     :length 1571 <environment>
  ..@ envName   : chr "m5_filtered_probesets_only"
  ..@ index2xy  :function (object, i)
  ..@ xy2index  :function (object, x, y)
  ..@ nrow      : int 732
  ..@ ncol      : int 732
  ..@ probeTypes: chr [1:2] "pm" "mm"
  ..@ chipType  : chr "hgu133a2cdf"


4) put 6 HG-U133a2 .CEL files into the working dir. and read cel files into 
workspace.

m5 <- ReadAffy()

str(m5)

Formal class 'AffyBatch' [package "affy"] with 9 slots
  ..@ cdfName    : chr "HG-U133A_2"
  ..@ nrow       : int 732
  ..@ ncol       : int 732
  ..@ exprs      : num [1:535824, 1:6]  128 6360  110 6760  112 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : NULL
  .. .. ..$ : chr [1:6] "199.CEL" "200.CEL" "201.CEL" "202.CEL" ...
  ..@ se.exprs   : logi[0 , 0 ]
  ..@ phenoData  :Formal class 'phenoData' [package "Biobase"] with 2 slots
  .. .. ..@ pData.sample    : int [1:6] 1 2 3 4 5 6
  .. .. ..@ varLabels.sample: chr "arbitrary numbering"
  ..@ description:Formal class 'MIAME' [package "Biobase"] with 11 slots
  .. .. ..@ name          : chr ""
  .. .. ..@ lab           : chr ""
  .. .. ..@ contact       : chr ""
  .. .. ..@ title         : chr ""
  .. .. ..@ abstract      : chr ""
  .. .. ..@ url           : chr ""
  .. .. ..@ samples       : list()
  .. .. ..@ hybridizations: list()
  .. .. ..@ normControls  : list()
  .. .. ..@ preprocessing :List of 2
  .. .. .. ..$ filenames  :List of 6
  .. .. .. .. ..$ : chr "/199.CEL"
  .. .. .. .. ..$ : chr "/200.CEL"
  .. .. .. .. ..$ : chr "/201.CEL"
  .. .. .. .. ..$ : chr "/202.CEL"
  .. .. .. .. ..$ : chr "/203.CEL"
  .. .. .. .. ..$ : chr "/204.CEL"
  .. .. .. ..$ affyversion: chr NA
  .. .. ..@ other         : list()
  ..@ annotation : chr "hgu133a2"
  ..@ notes      : chr ""

5) set cdfName slot of m5 affybatch object to my CDF name..

m5 at cdfName <- "m5_CDF"

6) tried rma.

m5rma <- rma(m5)
Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) :
	Invalid object for as.environment

7) tried gcrma

library(gcrma)
m5gcrma <- gcrma(m5)
Computing affinities[1] "Checking to see if your internet connection 
works..."
Note: You did not specify a download type.  Using a default value of: Source
This will be fine for almost all users

Error in getCDF(cdfpackagename) : Environment m5cdfcdf was not found in the 
Bioconductor repository.


I'm not sure how to either set the environment for rma, or set 
cdfpackagename for gcrma...?

The aforementioned tutorial was great for how to create the CDF, but after 
that I can't seem to find out any more information on what to do next as far 
as normalization goes...

Thanks for any help,
Ken