Hey James,

Thanks for your answer, I'll look into your suggestions...

However just to be sure, is there an 'easy' hack to get the probes out of
the CDF file and match them to the CEL file information?

I have available found the following files that describe the array:
cdf.gz
desc.txt.gz
mapping.txt.gz
probe_tab.txt.gz

Just getting the probe locations or sequences is enough, then I could start
the analysis myself
(either by mapping probes to the reference using blast, or using the
supplied locations),

I was hoping that I could use the Affy package for normalization of probe
intensities, etc

Gr,
Danny



2014-06-02 21:49 GMT+02:00 James W. MacDonald <jmacdon@uw.edu>:

> Hi Danny,
>
>
> In general, you don't use the makecdfenv/affy pipeline for tiling arrays,
> as there aren't (to my knowledge) any probesets. Instead, there are just
> probes, tiled along the genome.
>
> The affy package is predicated upon the idea that a set of probes are all
> grouped into a probeset, which is intended to measure the expression of a
> transcript. Since the tiling arrays are completely different, the two don't
> really mix.
>
> Normally I would point you to the oligo package, but you need to build a
> pdInfoPackage, which expects a bpmap file, not a cdf. In addition, I tried
> to read in the cdf that you can get from GEO using readCdfUnits() from
> affxparser, and it consistently segfaulted, so there might be a problem
> with the cdf itself.
>
> Looking around, it appears you might be better served by using either
> aroma (http://www.aroma-project.org/), which is supposed to handle tiling
> arrays (but since aroma uses affxparser, maybe it won't work).
>
> Or you could try Affy's software:
>
> http://www.affymetrix.com/estore/partners_programs/programs/developer/
> TilingArrayTools/index.affx
>
> Best,
>
> Jim
>
>
>
>
> On 6/2/2014 2:55 PM, Danny Arends wrote:
>
>> Hey,
>>
>> I got a bug trying to create a custom cdf environment, which I need to
>> analyse some affy arrays:
>>
>> Both functions give the same error:
>>
>>  > make.cdf.package("GPL16303_TilingatSNPtilx520433_At_TAIRG.cdf",
>> species="Arabidopsis_Thaliana")
>> Reading CDF file.
>> Creating CDF environment
>> Wait for about 0 dots
>> Error in assign(x[i], value[[i2]], envir = envir, inherits = inherits) :
>>    invalid first argument
>>
>>  > env <- make.cdf.env("GPL16303_TilingatSNPtilx520433_At_TAIRG.cdf")
>> Reading CDF file.
>> Creating CDF environment
>> Wait for about 0 dots
>> Error in assign(x[i], value[[i2]], envir = envir, inherits = inherits) :
>>    invalid first argument
>>
>> My R version:
>>  > version
>> platform       x86_64-pc-linux-gnu
>> arch           x86_64
>> os             linux-gnu
>> system         x86_64, linux-gnu
>> status
>> major          3
>> minor          1.0
>> year           2014
>> month          04
>> day            10
>> svn rev        65387
>> language       R
>> version.string R version 3.1.0 (2014-04-10)
>> nickname       Spring Dance
>>
>> Is there any fix for this???, because I really wanna look into my array
>> data...
>>
>> Gr,
>> Danny Arends
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

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