hello,

i'm new to bioconductor and processing array data, but i'm not new to R 
- not an expert, either, let's say mildly competent...

(output of sessionInfo() is at bottom of this email.)

the short version of my question:
i'm having trouble running gcrma() on an affy batch object returned from 
combineAffyBatch(). the combined object is created by combining data 
from two types of mouse chips: moe430a and mouse4302. gcrma() returns 
this error:

 > gcrma.eset.A.V2 <- gcrma(comb.A.V2$dat)

 Adjusting for optical effect...Done.

 Computing affinitiesError in getCDF(cdfpackagename) : The current operation could not 
 access the Bioconductor repository. Please check your internet connection, and report 
 further problems to bioconductor@stat.math.ethz.ch


the long version of my question, and more code:
i believe the combining of chip data occurs without error. i put the 
newly computed cdf in the global environment - i think this is where the 
problem is - like it's not being recognized.

> library(mouse4302cdf)  

> library(moe430acdf)

> comb.A.V2 <- combineAffyBatch(list(A,V2),c("moe430aprobe",
  "mouse4302probe"),newcdf="comb.430a.4302.cdf")

 package:moe430aprobe    moe430aprobe    

 package:mouse4302probe  mouse4302probe  

 245487 unique probes in common

# put new cdf in global environment

> comb.430a.4302.cdf <- comb.A.V2$cdf

> library(gcrma)

  Loading required package: splines

> gcrma.eset.A.V2.3 <- gcrma(comb.A.V2$dat)

  Adjusting for optical effect...Done.

  Computing affinitiesError in getCDF(cdfpackagename) : The current operation could not 
  access the Bioconductor repository. Please check your internet connection, and report 
  further problems to bioconductor@stat.math.ethz.ch

------
when i check the cdf of the combined object, it looks correct to me:


> cdfName(comb.A.V2$dat)

[1] "comb.430a.4302.cdf"


--------------------

 > sessionInfo()
R version 2.4.1 (2006-12-18)
i386-pc-solaris2.10

locale:
/en_US.ISO8859-1/C/C/en_US.ISO8859-1/en_US.ISO8859-1/C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"   
[7] "datasets"  "methods"   "base"    

other attached packages:
 hgu95av2probe    hgu95av2cdf      hgu95acdf mouse4302probe   moe430aprobe
         "1.0"        "1.4.3"        "1.4.1"       "1.14.0"       "1.14.0"
         gcrma     moe430acdf   mouse4302cdf    matchprobes           affy
       "2.6.0"       "1.14.0"       "1.14.0"        "1.6.0"       "1.12.2"
        affyio        Biobase
       "1.2.0"       "1.12.2"

i've searched the email list (what i think is) extensively and although 
i've found other mentions of similar problems i haven't stumbled across 
a solution that works for me. in particular, i tried a fairly different 
approach that involved creating affinity info objects and that didn't 
work either (i can supply the error of that attempt if necessary). the 
method i tried is described here 
<http://thread.gmane.org/gmane.science.biology.informatics.conductor/2500/focus=2747>.

thanks in advance for any and all help,
mike

-- 
Michael Palumbo					palumbo@wadsworth.org
Bioinformatics Core	           Genomics Institute: (518) 880-1360
Wadsworth Center		 Center for Med. Sci.: (518) 402-4587
Center for Medical Science
New York State Dept of Health
150 New Scotland Ave
Albany, NY 12208


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