[BioC] How to generate the CDF files for Arabidopsis Tiling Arrays

[Naira Naouar]

Hi Zhen,


The Arabidopsis tiling 1.0R cdf that I generated is available here:
ftp://ftp.psb.ugent.be/pub/nanao/athtiling1.0rcdf_1.0.1.tar.gz

this CDF contains 29670 probesets and was created on a unix environment.

If you are analysing tiling arrays in R, you must make sure that you
have enough memory available
To make use of the package those are the instructions:
In R:

library(affy)
library(athtiling1.0rcdf)
data<-ReadAffy()
data at cdfName<-"athtling1.0rcdf"

Then use rma or mas5 to preprocess your data (gcrma is not possible
because I did not create the probe file).

Good luck with your analysis.
If you have any problem with the package (installation or any), feel
free to contact me.
To install a R package in unix, : R CMD INSTALL 
athtiling1.0rcdf_1.0.1.tar.gz /path/R/libraries

Best,
Naira


zhen tao wrote:
> Dear all,
>
> I'm new to R programming and Bioconductor. Recently I'm trying to analyze
> the data of Arabidopsis Tiling Array using Bioconductor. However, I noticed
> that the CDF files should be included when importing the CEL files so that
> we can do the QC or RMA studies. But there's no cdf/probe package files for
> this tiling array ( only for ATH1). I have downloaded the files named
> attltiling10rattaircdf_10.0.0.tar and attltiling10rattairprobe_10.0.0.tar
> somewhere. May I know if these files can be used as the tiling array cdf
> since the R keeps displaying the message
>  Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain At35b_MR_v04
> Library - package at35bmrv04cdf not installed
> Bioconductor - at35bmrv04cdf not available
>
> If not, is there anyway I can do to generate the cdf file for this tiling
> array?
>
> thanks,
> Tao Zhen
>
> 	[[alternative HTML version deleted]]
>
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-- 
==================================================================
Naïra Naouar 

Tel:+32 (0)9 331 38 63
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
nanao at psb.vib-ugent.be                         http://www.psb.vib-ugent.be