Question

How To Save A Cdf Environment In A File ?

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11.9 years ago

Mycroft34 ▴ 120

To analyze Affymetrix chips, one can either load a chip description file (cdf) from bioconductor (example: hgu133plus2cdf), or create one using the bioconductor package makecdfenv from the corresponding Affymetrix cdf file (here: HG-U133Plus2.cdf). The result is an environment as a hashtable, with the probesets as keys, and a table of probes as value (at least it is what I understood).

After modifying the composition of the cdf (removing unwanted probes and probesets), I would like the resulting environment to be packaged or saved as a file (to give it to the final user, and be sure that it will be used instead of the original cdf). makecdfenv (make.cdf.package) allow one to produce a package from a file; but how should I save the modified environment in a file to be able to use that function.

Thanks for any hint.

bioconductor • 3.8k views

ADD COMMENT • link 11.9 years ago by Mycroft34 ▴ 120

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Did you try saving it to a file with save( )?

ADD REPLY • link 11.9 years ago by Obi Griffith 20k

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Yes; but when reloaded it is not recognized as a true cdf by bioconductor rma or similar packages, that keep on searching for the original package; but I found an alternative with Array Initiative programme. I still have to understand how to save properly my modified cdf environment, but there is no hurry.

ADD REPLY • link 11.9 years ago by Mycroft34 ▴ 120

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Hmm. I see. I searched around on this topic and saw several people posting over the years a similar question. It seems that somehow using makecdfenv should be possible. But, I did not see a clear solution anywhere. So, if anyone else has successfully done this it would be great if they will post here.

ADD REPLY • link 11.9 years ago by Obi Griffith 20k

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makecdfenv is the end solution; but it requires a file properly formatted; in fact, it is exactly what ArrayInitiative (http://wellerlab.uncc.edu/ArrayInitiative/tutorial.html) is doing : taking the ascii cdf file originally proposed by Affymetrix as well as the corresponding probe file, to produce a dat file that your can then filter out of the unwanted probes and probesets. after reloading in ArrayInitiative the modified dat file, the programme output the modified ascii cdf file, that can then be used to produce a package with makecdfpackage from makecdfenv, or directly produce with the same package an environment usable in the subsequent array processing.

ADD REPLY • link 11.9 years ago by Mycroft34 ▴ 120

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Very cool. It seems like this solved your problem. I suggest you put these details in an answer to your own question. You'll get my upvote! And, then this question can have an accepted answer.

ADD REPLY • link 11.9 years ago by Obi Griffith 20k

score 3 · Answer 1 · 2013-01-31

To close that question, as suggested, here is a summary of the solution:

In order to use a custom cdf to analyse Affymetrix array, (for example, after removing unwanted probes or probesets), it is necessary to create a cdf file for example, from a cdf environment from bioconductor, or generated from an ascii cdf file given by Affymetrix.

The package makecdfenv is the end solution, that uses a file properly formatted.

I found 2 solutions to create that file;

The easiest is using a program from Array Initiative (http://wellerlab.uncc.edu/ArrayInitiative/index.html) :

Taking the ascii cdf file originally proposed by Affymetrix as well as the corresponding probe file, the program produced a dat file that your can then filter out of the unwanted probes and probesets. after reloading in ArrayInitiative the modified dat file, the program output the modified ascii cdf file, that can then be used to produce a package with makecdfpackage from makecdfenv, or directly produce with the same package an environment usable in the subsequent array processing. This solution worked perfectly for me.

For a more detailled procedure, there is a step by step tutorial at : http://wellerlab.uncc.edu/ArrayInitiative/tutorial.html

Since then, I found another solution given at aroma project : http://www.aroma-project.org/node/41 This solution that I briefly tested uses env2Cdf, an undocumented function from aroma.affymetrix package. It seemed to work; the cdf file produced is a binary one.