[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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