[BioC] makecdfenv package bug

James W. MacDonald jmacdon at uw.edu
Mon Jun 2 21:49:06 CEST 2014


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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