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

[Wolfgang Huber]

Dear Tao Zhen

for transcript mapping, you could have a look at the papers cited below, 
and the vignettes of the "tilingArray" package. But this is not the only 
way to do it, and it will not work for you out of the box, you will need 
to spend effort on adapting it to your arrays and your experimental design.

Huber W., Toedling J., Steinmetz L. M. (2006) Transcript mapping with 
high-density oligonucleotide tiling arrays. Bioinformatics 22(16): 
1963-1970.

Antisense artifacts in transcriptome microarray experiments are resolved 
by actinomycin D. Perocchi F, Xu Z, Clauder-Münster S, Steinmetz LM.
Nucleic Acids Res. 2007;35(19):e128. PMID: 17897965

Best wishes
      Wolfgang

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




zhen tao wrote:
> Dear Dr.Huber:
> 
> Sorry I didn't make my question clearly enough since it's the first I'm 
> dealing with this tiling array. It seems that it's not that easy as I 
> thought.
> 
> My experiment is trying to use arabidopsis tiling array(1.0R)  to do the 
> whole transcriptome mapping, especially for identifying new transcripts, 
> so it's kind of expression level study. I'm performing some analysis 
> referring to your book <Bioconductor Case Study>. However, I just cannot 
> go further after importing the CEL files since I couldn't find the CDF 
> files for this type of tiling array.  It would be really thankful if you 
> can give some suggestions.
> 
> 
> best regards,
> Tao Zhen
> Plant Functional Genomics Group
> Department of Biological Sciences
> National University of Singapore
> 
> On Thu, Mar 5, 2009 at 5:02 AM, Wolfgang Huber <huber at ebi.ac.uk 
> <mailto:huber at ebi.ac.uk>> wrote:
> 
>     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
> 
>     ----------------------------------------------------
>     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]]
> 
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