[BioC] GCRMA error

[Puhong Gao]

Hi, Zhijin,

I don't  see "rnu34probe" and other chip packages (see below)

> search()
 [1] ".GlobalEnv"          "package:splines"     "package:gcrma"
 [4] "package:matchprobes" "package:affy"        "package:reposTools"
 [7] "package:Biobase"     "package:tools"       "package:methods"
[10] "package:stats"       "package:graphics"    "package:grDevices"
[13] "package:utils"       "package:datasets"    "Autoloads"
[16] "package:base"
>

I just tried GCRMA  on RG U34a data and it worked without a problem (see 
below). (R was started in a different folder, if it means anything.). So, it 
should be rnu34 chip specific.

> local({pkg <- select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Loading required package: affy
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: reposTools
Loading required package: matchprobes

> search()
 [1] ".GlobalEnv"          "package:gcrma"       "package:matchprobes"
 [4] "package:affy"        "package:reposTools"  "package:Biobase"
 [7] "package:tools"       "package:methods"     "package:stats"
[10] "package:graphics"    "package:grDevices"   "package:utils"
[13] "package:datasets"    "Autoloads"           "package:base"
> g.so<-gcrma(so)
Computing affinities.Done.
Adjusting for optical effect..............................Done.
Adjusting for non-specific binding..............................Done.
Normalizing
Calculating Expression
>

Best,

Puhong

----- Original Message ----- 
From: "Zhijin Wu" <zwu at jhsph.edu>
To: "Puhong Gao" <pgao at hunter.cuny.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Tuesday, May 10, 2005 5:15 PM
Subject: Re: [BioC] GCRMA error


> Do you see "rnu34probe" when you do
>
> search()
>
> If yes, what do you get if you do
>
> P <-get("rnu34probe")
>