[BioC] Importing CDF file for custom array using makecdfenv

Jenny Drnevich drnevich at uiuc.edu
Wed Nov 8 23:49:18 CET 2006


Hi Jim & others,

I'm at my wit's end - I really cannot figure out anything I am doing wrong 
in trying to create an environment for a custom Affy array.  It seems I'm 
having the same problem as in this thread, but the solution Jim suggested 
isn't working. I've followed the makecdfenv vignette, sections 3 and 4 (I'm 
following the advice to skip trying to make a package on a PC, for now). 
Here's what I've tried:


R version 2.4.0 (2006-10-03)
Copyright (C) 2006 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
#deleting most of intro

 > setwd("C:/Statistics/Clayton")

 > source("http://bioconductor.org/biocLite.R")

 > biocLite("makecdfenv")

Running getBioC version 0.1.8 with R version 2.4.0
Running biocinstall version 1.9.9 with R version 2.4.0
Your version of R requires version 1.9 of Bioconductor.
trying URL 
'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/makecdfenv_1.12.0.zip'
Content type 'application/zip' length 3307506 bytes
opened URL
downloaded 3229Kb

package 'makecdfenv' successfully unpacked and MD5 sums checked

The downloaded packages are in
         C:\Documents and Settings\drnevich\Local 
Settings\Temp\RtmpCw5Rqb\downloaded_packages
updating HTML package descriptions

 > library(makecdfenv)

 > cleancdfname(whatcdf("p0601_51.CEL"))

Error in .Call("ReadHeader", filename, compress, PACKAGE = "affy") :
         C symbol name "ReadHeader" not in DLL for package "affy"


I HOPE all the trouble I'm having below is related to this, and not to me! 
Because the 'whatcdf' isn't working, I tried to get the cdf name from an 
AffyBatch object:

 > raw <- ReadAffy()

 > raw at cdfName
[1] "lund-zfa530237N"

 > cleancdfname(raw at cdfName)  # the makecdf vignette says 'getCdfInfo' will 
look for an environment by this name for the AffyBatch
[1] "lundzfa530237ncdf"

 > lundzfa530237ncdf <- make.cdf.env("lund-zfa530237N.cdf")
Reading CDF file.
Creating CDF environment
Wait for about 231 
dots...............................................................................................................................................................................................................................

 > length(ls(lundzfa530237ncdf))  #from the help file of 'make.cdf.env", so 
I think it's been created properly...
[1] 23136

# ...but...
 > raw
Error in getCdfInfo(object) : Could not obtain CDF environment, problems 
encountered:
Specified environment does not contain lund-zfa530237N
Library - package lundzfa530237ncdf not installed
Data for package affy did not contain lundzfa530237ncdf
Bioconductor - lundzfa530237ncdf not available
AffyBatch object
size of arrays=754x754 features (53306 kb)
cdf=lund-zfa530237N (??? affyids)
number of samples=12
Error in getCdfInfo(object) : Could not obtain CDF environment, problems 
encountered:
Specified environment does not contain lund-zfa530237N
Library - package lundzfa530237ncdf not installed
Data for package affy did not contain lundzfa530237ncdf
Bioconductor - lundzfa530237ncdf not available
In addition: Warning message:
missing cdf environment ! in: show(<S4 object of class "AffyBatch">)

I searched the archives and found this thread from Jim about the seemingly 
same error:

 >> I do not get any errors, but when I try to look at the affybatch object
 >> get the following message:
 >>
 >> Error in getCdfInfo(object) : Could not obtain CDF environment, problems
 >> encountered:
 >> specified environment does not contain XXX Library - package XXXcdf not
 >> installed Data for package affy did not contain XXXcdf Bioconductor -
 >> XXXcdf not available AffyBatch object size of arrays=291x291 features
 >> (15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in
 >> getCdfInfo(object) : Could not obtain CDF environment, problems
 >> encountered:
 >> Specified environment does not contain XXX
 >
 >This line is a hint, although rather oblique. When the affy package
 >looks for an environment in the current .GlobalEnv, it expects it to be
 >named XXX, so if you use make.cdf.env, you should name it XXX.

OK, so this is contrary to what it says in the vignette, but I try it anyway:

 > rm(lundzfa530237ncdf)
 > lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf")
Reading CDF file.
Creating CDF environment
Wait for about 231 
dots....................................................................................................................................................................................................................................................

But still no luck!

 > raw
Error in getCdfInfo(object) : Could not obtain CDF environment, problems 
encountered:
Specified environment does not contain lund-zfa530237N
Library - package lundzfa530237ncdf not installed
Data for package affy did not contain lundzfa530237ncdf
Bioconductor - lundzfa530237ncdf not available
AffyBatch object
size of arrays=754x754 features (53306 kb)
cdf=lund-zfa530237N (??? affyids)
number of samples=12
Error in getCdfInfo(object) : Could not obtain CDF environment, problems 
encountered:
Specified environment does not contain lund-zfa530237N
Library - package lundzfa530237ncdf not installed
Data for package affy did not contain lundzfa530237ncdf
Bioconductor - lundzfa530237ncdf not available
In addition: Warning message:
missing cdf environment ! in: show(<S4 object of class "AffyBatch">)

Am I doing anything wrong? I can't figure out what it could be for the life 
of me!!! Contents of workspace and sessionInfo below.

Thanks,
Jenny



 > ls()
  [1] "biocinstall"               "biocinstall.affyPkgs"
  [3] "biocinstall.allPkgs"       "biocinstall.defaultPkgs"
  [5] "biocinstall.graphPkgs"     "biocinstall.litePkgs"
  [7] "biocinstall.monographPkgs" "biocLite"
  [9] "lundzfa530237n"                "raw"

 > sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
    makecdfenv  affyQCReport    simpleaffy         made4 scatterplot3d
      "1.12.0"      "1.12.0"       "2.8.0"       "1.8.0"      "0.3-24"
          ade4       affyPLM         gcrma   matchprobes      affydata
       "1.4-2"      "1.10.0"       "2.6.0"       "1.6.0"      "1.10.0"
affycoretools       biomaRt         RCurl           XML       GOstats
       "1.6.0"       "1.8.0"       "0.7-0"     "0.99-93"       "2.0.0"
      Category    genefilter      survival          KEGG          RBGL
       "2.0.0"      "1.12.0"        "2.29"      "1.14.0"      "1.10.0"
      annotate            GO         graph         limma          affy
      "1.12.0"      "1.14.0"      "1.12.0"       "2.9.1"      "1.12.0"
        affyio       Biobase       RWinEdt
       "1.2.0"      "1.12.2"       "1.7-5"
 >




> > I do not get any errors, but when I try to look at the affybatch object
> > I get the following message:
> >
> > Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> > encountered:
> > Specified environment does not contain XXX Library - package XXXcdf not
> > installed Data for package affy did not contain XXXcdf Bioconductor -
> > XXXcdf not available AffyBatch object size of arrays=291x291 features
> > (15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in
> > getCdfInfo(object) : Could not obtain CDF environment, problems
> > encountered:
> > Specified environment does not contain XXX
>
>This line is a hint, although rather oblique. When the affy package
>looks for an environment in the current .GlobalEnv, it expects it to be
>named XXX, so if you use make.cdf.env, you should name it XXX. However,
>if it looks for a package, it has to be named xxxcdf. The best bet is to
>allow make.cdf.package to do the package naming itself, because it will
>be 100% correct.
>
> >
> > I have tried putting the CDF file (created by BioC) in the R libraries
> > folder with other libraries, but no luck.
>
>Nope. You have to install. This would have worked for maybe R-1.7.0 or
>so, but modern versions of R require you to install the right way.
>
>HTH,
>
>Jim
>
> >
> > In the makecdfenv vignette it says to "open a terminal with an operating
> > system shell and write R CMD INSTALL XXXcdf", but I don't know how to do
> > this on windows.
> >
> > Any suggestions would be greatly appreciated!
> >
> > Ann
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > --------------------------------------------------------
> >
> >
> > This email is confidential and intended solely for the use o...{{dropped}}
> >
> > _______________________________________________
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>
>--
>James W. MacDonald, M.S.
>Biostatistician
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
>734-647-5623
>
>
>**********************************************************
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu



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