[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
> >
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
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> >
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> >
> >
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> >
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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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