[BioC] Importing CDF file for custom array using makecdfenv
Jenny Drnevich
drnevich at uiuc.edu
Thu Nov 9 16:48:09 CET 2006
Hi all,
Thanks Jim and Kasper for your responses. I'm still having trouble, and I
have a suggestion for changing the makecdfenv vignette...
>>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"
>
>Note here what the cdfname is. The affy package will look for this *exact*
>name when looking for the environment. Below, you call it something else:
>
> > lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf")
>
>If you name it lund-zfa530237N, then everything should be copacetic.
The reason I tried naming it "lundzfa530237ncdf" and then "lundzfa530237n",
not "lund-zfa530237N" is because the vignette, under Section 4, Naming of
CDF Packages and Environments, specifically says:
"The method getCdfInfo takes as an argument AffyBatch and returns the
appropriate environment. If x is an AffyBatch, this function will look for
an environment with name cleancdfname(x at cdfName)."
Perhaps this should be changed? At any rate, I tried naming it
"lund-zfa530237N", but the "-" in the name is messing everything up:
> raw at cdfName
[1] "lund-zfa530237N"
> lund-zfa530237N <- make.cdf.env("lund-zfa530237N.cdf")
Reading CDF file.
Creating CDF environment
Wait for about 231
dots............................................................................................................................................................................................................................................
Error in lund - zfa530237N <- make.cdf.env("lund-zfa530237N.cdf") :
object "lund" not found
> length(ls(lund-zfa530237N))
Error in try(name) : object "lund" not found
Error in as.environment(pos) : no item called "lund - zfa530237N" on the
search list
So I decided just to change raw at cdfName to "lundzfa530237n" as a work
around for now. I probably won't be seeing any more experiments using this
custom array, although I would like to make a cdf package for it. That's
another long story... I thought I had everything needed because I had
compiled some code successfully with R 2.3.0, but I'm not able to make the
cdf package. We're installing R on our new blade system next week, so I'll
just wait for that!
Thanks,
Jenny
>I know this is a PITA. Seth looked at making the naming consistent around
>the time I wrote the email you quote below, and for some reason (I forget
>now what it was) fixing it was way more difficult than one might think it
>would be, especially considering that it is not very common to use an
>unpackaged environment.
>
>Have you considered making a cdf package? Using an env is OK, but it isn't
>as persistent as a package would be (plus you will automatically get the
>correct name using make.cdf.package()).
>
>
>HTH,
>
>Jim
>
>
>> > 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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>>>
>>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>>--
>>>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
>>>
>>>
>>>**********************************************************
>>>Electronic Mail is not secure, may not be read every day, and should not
>>>be used for urgent or sensitive issues.
>>>
>>>_______________________________________________
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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
>>Search the archives:
>>http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>--
>James W. MacDonald
>University of Michigan
>Affymetrix and cDNA Microarray Core
>1500 E Medical Center Drive
>Ann Arbor MI 48109
>734-647-5623
>
>
>
>**********************************************************
>Electronic Mail is not secure, may not be read every day, and should not
>be used for urgent or sensitive issues.
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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