[BioC] error ReadAffy

Wed Feb 5 18:13:41 CET 2014

Hi Nu,

Well, if I google gpl17417, I end up at this page:

http://165.112.7.19/geo/query/acc.cgi?acc=GPL17417

which indicates that this is just an AraGene 1.1 ST array that they used 
a MNBI re-mapped cdf, from their version 16 set of packages. So now if I 
go there:

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp

I see this:

*Version 16 (Data Sources 
<http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/version.html>)*
Sep 27, 2012, version 16 is released
Custom CDF 	R 2.15, BioC 2.11

So you could hypothetically use an old version of R and BioC. However, I 
prefer to stay in the here and now, so let's see what we can do:

 > library(BiocInstaller)
Bioconductor version 2.12 (BiocInstaller 1.10.4), ?biocLite for help
A newer version of Bioconductor is available for this version of R,
?BiocUpgrade for help
 > biocLite(c("aragene11stattairgcdf","aragene11stattairgprobe"))
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.1.
Installing package(s) 'aragene11stattairgcdf' 'aragene11stattairgprobe'
Warning message:
packages ‘aragene11stattairgcdf’, ‘aragene11stattairgprobe’ are not 
available (for R version 3.0.1)

Hmmm. That's pretty bootleg. The MNBI site claims that version 17 works 
with BioC 2.12:

*Version 17 (Data Sources 
<http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.0.0/version.html>)*
Apr 25, 2013, version 17 is released
Custom CDF 	R 2.15, BioC 2.11 	R 3.0, BioC 2.12

In that case let's switch to R-3.0.2 and install by hand:

 > 
download.file("http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.1.0/tairg.download/aragene11stattairgcdf_17.1.0.tar.gz", 
"./aragene11stattairgcdf_17.1.0.tar.gz")
trying URL 
'http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.1.0/tairg.download/aragene11stattairgcdf_17.1.0.tar.gz'
Content type 'application/x-gzip' length 2258039 bytes (2.2 Mb)
opened URL
==================================================
downloaded 2.2 Mb

 > 
download.file("http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.1.0/tairg.download/aragene11stattairgprobe_17.1.0.tar.gz", 
"./aragene11stattairgprobe_17.1.0.tar.gz")
trying URL 
'http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.1.0/tairg.download/aragene11stattairgprobe_17.1.0.tar.gz'
Content type 'application/x-gzip' length 6983531 bytes (6.7 Mb)
opened URL
==================================================
downloaded 6.7 Mb

 > 
install.packages(c("aragene11stattairgprobe_17.1.0.tar.gz","aragene11stattairgcdf_17.1.0.tar.gz"), 
repos=NULL)
* installing *source* package ‘aragene11stattairgprobe’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (aragene11stattairgprobe)
* installing *source* package ‘aragene11stattairgcdf’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (aragene11stattairgcdf)

Now I don't see any celfiles on GEO to test, and to use gcrma will take 
some effort, as I already stated, but I can now at least run RMA on 
these data using the affy package with the re-mapped cdf.

And if I just want to use oligo, I can

 > biocLite("pd.aragene.1.1.st")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2.
Installing package(s) 'pd.aragene.1.1.st'
trying URL 
'http://bioconductor.org/packages/2.13/data/annotation/src/contrib/pd.aragene.1.1.st_3.8.0.tar.gz'
Content type 'application/x-gzip' length 34310175 bytes (32.7 Mb)
opened URL
==================================================
downloaded 32.7 Mb

* installing *source* package ‘pd.aragene.1.1.st’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pd.aragene.1.1.st)

The downloaded source packages are in
‘/tmp/RtmpMlVUZN/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
 >

Best,

Jim

On 2/5/2014 11:24 AM, n omranian wrote:
>
> Hi Jim,
>
> Thanks for the reply.
>
> yes, this is a warning but when I use exp_data <- gcrma(affydata), it 
> gives me this error.
>
> Also if I use oligo, I couldn't find a way to map my probe ids. I mean 
> I have the CDF file, but it is useless. So, the most important thing 
> for me is the mapping and applying normalization on my affy data.
>
>
> Adjusting for optical effect..............................Done.
> Computing affinities[1] "Checking to see if your internet connection 
> works..."
> [1] "Environment gpl17417aragene10stattairgcdfcdf was not found in the 
> Bioconductor repository."
> [1] "Checking to see if your internet connection works..."
> [1] "Environment gpl17417aragene10stattairgcdfprobe was not found in 
> the Bioconductor repository."
> Error in get(probepackagename) :
> object 'gpl17417aragene10stattairgcdfprobe' not found
>
>
> Thanks,
> Nu
>
>
>
> On Wednesday, February 5, 2014 5:18 PM, James W. MacDonald 
> <jmacdon at uw.edu> wrote:
> Hi Nu,
>
> On 2/5/2014 9:42 AM, n omranian wrote:
> > Hi All,
> >
> > I have a problem reading my cel files.
> > My data is from Arabidopsis thaliana and the platform is GPL17417.
> >
> > I get the cdf file for this platform, which is 
> GPL17417_aragene10st_At_TAIRG and installed it in R.
> >
> > But still when I read the cel files I get the error as follows:
> >> affydata <- ReadAffy(cdfname="gpl17417aragene10stattairgcdf")
> >
> > Warning message:
> >
> >
> >
> > The affy package can process data from the Gene ST 1.x series of arrays,
> > but you should consider using either the oligo or xps packages, 
> which are specifically
> > designed for these arrays.
>
> That's not an error. It's a warning. Is there something about this
> warning that is unclear? The goal is to explain that you should really
> be using oligo or xps for these arrays.
>
> >
> >
> > and when I use read.affy (simpleaffy) it gives me this error:
> > read.affy() Error in file(file, "rt") : cannot open the connection 
> In addition: Warning message: In file(file, "rt") : cannot open file 
> './covdesc': No such file or directory
> >
> > I want to read my cel files and normalize them with gcrma.
>
> The simpleaffy error is insurmountable, as simpleaffy is designed
> specifically for 3'-biased arrays. If you want to do quality control,
> perhaps you should try the arrayQualityMetrics package.
>
> In addition, using gcrma with PM-only arrays is not a trivial task.
> Unless you are willing to do the research to figure out how to do it, I
> would recommend you follow the warning above and use oligo or xps to
> analyze these data.
>
> Best,
>
> Jim
>
>
>
> >
> > I would appreciate if anybody could help me.
> > Thanks,
> > Nu
>
> >
> > [[alternative HTML version deleted]]
> >
> >
> >
> > _______________________________________________
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> > Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099