[BioC] .cel file processing is not working for an old array

[James W. MacDonald]

Hi Maria,

Sean and Martin have already given you feedback about updating your 
AnnotationDbi package, so I won't comment further on that issue. But I 
will note that the for() loop you are using below is almost surely not 
what you want to be doing.

The RMA algorithm uses information from all arrays in an experiment to 
help generate expression values. By running rma() individually on each 
array, you are eliminating that (very important) aspect of the algorithm.

The conventional thing to do is

setwd("/home/maria/Documents/Work with Pietro/Prostate Cancer")
Data<-ReadAffy()
eset <- rma(Data)

and then the ExpressionSet will contain normalized data for all nine arrays.

But this makes an assumption that these arrays are all from the same 
experiment, so a quantile normalization makes sense. If they are not all 
from the same experiment, or you have other reasons to suspect that a 
quantile normalization for all arrays is not sensible, you should 
instead be using the frma package, which is designed to allow you to 
process samples singly using the RMA algorithm.

Best,

Jim


On 7/26/2014 6:38 PM, Maria Kesa wrote:
> *Hello,*
>
>
> *I am trying to process very old .cel files from here:
> http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75
> <http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75>*
>
> *I have the newest version of R and updated BiocLite. *
> With the following code I get the error:
> library(affy)
> setwd("/home/maria/Documents/Work with Pietro/Prostate Cancer")
> for (i in 1:9) {
>    obj_name<-paste('N0',i,'__normal.CEL',sep="")
>    Data<-ReadAffy(filenames=obj_name)
>    eset<-rma(Data)
>    filename<-paste('sample',i,'.txt',sep="",collapse="")
>    write.exprs(eset, file=filename, sep="\t")
> }
>
> trying URL '
> http://bioconductor.org/packages/2.13/data/annotation/src/contrib/hgu95av2cdf_2.13.0.tar.gz
> '
> Content type 'application/x-gzip' length 1341545 bytes (1.3 Mb)
> opened URL
> ==================================================
> downloaded 1.3 Mb
>
> * installing *source* package ‘hgu95av2cdf’ ...
> ** R
> ** data
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Error : .onLoad failed in loadNamespace() for 'hgu95av2cdf', details:
>    call: NULL
>    error: package ‘AnnotationDbi’ was built before R 3.0.0: please
> re-install it
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing ‘/home/maria/R/x86_64-pc-linux-gnu-library/3.0/hgu95av2cdf’
>
> The downloaded source packages are in
>      ‘/tmp/RtmpRETXHh/downloaded_packages’
>   Show Traceback
>
>   Rerun with Debug
>   Error in getCdfInfo(object) :
>    Could not obtain CDF environment, problems encountered:
> Specified environment does not contain HG_U95Av2
> Library - package hgu95av2cdf not installed
> Library - package hgu95av2cdf not installed In addition: Warning message:
> In install.packages(cdfname, lib = lib, repos = biocinstallRepos(),  :
>    installation of package ‘hgu95av2cdf’ had non-zero exit status
>
> *When I try to install HG_U95Av2, I get the message:*
>
> biocLite("HG_U95Av2")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.1),
>    R version 3.0.2.
> Installing package(s) 'HG_U95Av2'
> Old packages: 'AnnotationDbi'
> Update all/some/none? [a/s/n]:
> a
> trying URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi_1.24.0.tar.gz
> '
> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb)
> opened URL
> ==================================================
> downloaded 4.1 Mb
>
> * installing *source* package ‘AnnotationDbi’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : package ‘DBI’ was built before R 3.0.0: please re-install it
> ERROR: lazy loading failed for package ‘AnnotationDbi’
> * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’
> * restoring previous ‘/usr/local/lib/R/site-library/AnnotationDbi’
>
> The downloaded source packages are in
>      ‘/tmp/RtmpRETXHh/downloaded_packages’
> Warning messages:
> 1: package ‘HG_U95Av2’ is not available (for R version 3.0.2)
> 2: In install.packages(update[instlib == l, "Package"], l, contriburl =
> contriburl,  :
>    installation of package ‘AnnotationDbi’ had non-zero exit status
>
> *When I try to install 'AnnotationDbi' I get*.
>
>> biocLite("AnnotationDbi")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.1),
>    R version 3.0.2.
> Installing package(s) 'AnnotationDbi'
> trying URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi_1.24.0.tar.gz
> '
> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb)
> opened URL
> ==================================================
> downloaded 4.1 Mb
>
> * installing *source* package ‘AnnotationDbi’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : package ‘DBI’ was built before R 3.0.0: please re-install it
> ERROR: lazy loading failed for package ‘AnnotationDbi’
> * removing ‘/home/maria/R/x86_64-pc-linux-gnu-library/3.0/AnnotationDbi’
>
> The downloaded source packages are in
>      ‘/tmp/RtmpRETXHh/downloaded_packages’
> Old packages: 'AnnotationDbi'
> Update all/some/none? [a/s/n]:
> a
> trying URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi_1.24.0.tar.gz
> '
> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb)
> opened URL
> ==================================================
> downloaded 4.1 Mb
>
> * installing *source* package ‘AnnotationDbi’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : package ‘DBI’ was built before R 3.0.0: please re-install it
> ERROR: lazy loading failed for package ‘AnnotationDbi’
> * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’
> * restoring previous ‘/usr/local/lib/R/site-library/AnnotationDbi’
>
> The downloaded source packages are in
>      ‘/tmp/RtmpRETXHh/downloaded_packages’
> Warning messages:
> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
>    installation of package ‘AnnotationDbi’ had non-zero exit status
> 2: In install.packages(update[instlib == l, "Package"], l, contriburl =
> contriburl,  :
>    installation of package ‘AnnotationDbi’ had non-zero exit status
>>
> *I would really aporeciate the help! *Is there any chance that I can parse
> these old .cel files?
>
> Thank you,
> Maria Kesa
>
> 	[[alternative HTML version deleted]]
>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099