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

Wolfgang Huber huber at ebi.ac.uk
Wed Mar 4 22:02:49 CET 2009

Dear Tao

Tiling arrays can be used for many things: transcript boundary mapping, 
new transcript discovery, DNA copy number variation, ChIP, genotyping, 
polymorphism discovery ... Different analysis approaches are needed for 
each of these questions (and only in some cases they are standardized 
enough that you can just run a Bioconductor package out of the box, 
without substantial work by yourself).

You did not even tell us what you want to do.

A CDF file (or package, environment) is necessary to form probe sets, 
needed for the rather narrow task of expression level analyses using 
annotated gene- or transcript structure. They will not help you for any 
of the tasks mentioned above.

Best wishes

Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber

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]]
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list