[BioC] How to generate the CDF files for Arabidopsis Tiling Arrays
nanao at psb.vib-ugent.be
Wed Mar 4 09:58:24 CET 2009
The Arabidopsis tiling 1.0R cdf that I generated is available here:
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:
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
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
> Tao Zhen
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