[BioC] Where can I get cdf? was(affy & problems with memory)

[James W. MacDonald]

Yi-Mo Deng wrote:
> Hi, I never analyzed affy data before, this is a silly question, but can 
> anyone tell me where to get the CDF file of Mus430_2.0? Or how can I 
> convert from CEL to CDF file?
> Someone did the array, but I could not find CDF from the files he sent 
> me.  Many thanks.

First, please don't send a response to an existing thread if you have a 
different question. Just send a new email with a reasonable subject 
line. This is actually the first guideline in the BioC posting guide:

http://www.bioconductor.org/docs/postingGuide.html

As for your question, if you need the actual cdf, then you can get it 
from Affy's website. If you need a cdf package to analyze the data, then 
you can either use biocLite() to get it directly, or easier still, you 
can just start analyzing the data using the affy package, and it will be 
downloaded automagically.

Note that the cdf (chip description file) simply maps probes to 
coordinates on the chip, whereas the cel file contains intensity values 
for each probe, so you cannot convert a cel file to a cdf.

HTH,

Jim



-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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