[BioC] error ReadAffy

[Hooiveld, Guido]

Hi Nu,
I noticed that the GEO accession number reflects an alternative (custom) CDF (chip definition file; mapping) of the AraGene10st array.
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL17417
The CDF file available at GEO cannot (directly) be used with BioC. You better download the custom CDF and corresponding probe file directly from the MBNI group (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v16), as is also indicated at the GEO web page. Note that the current version is 18.

Manhong (creator of the custom CDFs) and Benilton (author oligo package) said they are working on the implementation of the custom CDFs in the oligo framework. Until this is done, you can (should) use the affy library to read the data, and specify this CDF "aragene10stattairg" when calling ReadAffy() [affy.data <- ReadAffy(cdfname = "aragene10stattairg")].

Also, like Jim said, gcrma analysis with a PM-only array is rather complex and usually not done...

HTH,
Guido

--------------------------------------------------------- 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
email:      guido.hooiveld at wur.nl
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http://www.researcherid.com/rid/F-4912-2010


-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of n omranian
Sent: Wednesday, February 05, 2014 17:24
To: James W. MacDonald
Cc: bioconductor at r-project.org
Subject: Re: [BioC] error ReadAffy


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
>
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James W. MacDonald, M.S.
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