[BioC] RJpGene.1.0 and RCnGene.1.0 .CDF files

[James W. MacDonald]

Hi Ayelen,

On 7/3/2013 2:40 PM, Ayelen [guest] wrote:
> hello!
> I'm working with the RJpGene.1.0 and RCnGene.1.0 arrays from Affy and I can't find the .CDF files, where could I find them? is there a way to create them?

There are no cdf files for these arrays. Instead there are multiple 
files you will need. For each array you need:

1.) pgf, clf, mps files - these are included with the library files 
(e.g., 
http://www.affymetrix.com/Auth/analysis/downloads/lf/wt/RJpGene-1_0-st/RJpGene-1_0-st_rev01.zip 
for the Japanese rice). You have to unzip the file you download, and 
then start opening the subdirectories until you get to the very last 
one, and in there you will find these files.

2.) The annotation files 
(http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-32_2/RJpGene-1_0-st-v1.na33.2.irgsp1.transcript.csv.zip 
and 
http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-32_2/RJpGene-1_0-st-v1.na33.2.irgsp1.probeset.csv.zip 
for the Japanese rice).

If you want to use the oligo package, collect all these files in a 
single directory, and then install pdInfoBuilder using biocLite (and 
oligo, for that matter).

Then follow the instructions in this thread:

https://stat.ethz.ch/pipermail/bioconductor/2013-March/051335.html

You will of course need to substitute Rice and Oryza sativa for the 
organism and species.

Let us know if you get stuck.

Best,

Jim



> I only have the .CEL files.
>
> thanks!
> ayelén
>
>   -- output of sessionInfo():
>
> .
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099