[BioC] Importing CDF file for custom array using makecdfenv
Kasper Daniel Hansen
khansen at stat.Berkeley.EDU
Thu Nov 9 00:31:11 CET 2006
On Nov 8, 2006, at 2:49 PM, Jenny Drnevich wrote:
> 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"
This seems to be a bug in whatcdf: now all the IO routines have been
moved to affyio, so the .Call has to be ..., PACKAGE = "affyio".
CC'ed to the maintainer.
>
> 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.
If you look at the error message it seems you have a capitalization
issue - it seems as if the package is supposed to be called XXXncdf
(without "-"), but the environment is supposed to be called XXXN
(with "-"). However, my own experiences with makecdfenv and CDF names
are limited...
Kasper
> 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
>>>
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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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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