[BioC] error ReadAffy

[James W. MacDonald]

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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>
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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