Question: Creating a CDFenv without cdf file
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gravatar for Nicholas Lewin-Koh
13.6 years ago by
Nicholas Lewin-Koh430 wrote:
Hi, I have many cel files from a custom chip, but I do not have the cdf file. I do have the chip design information and and the seqence information but they are in seperate text files. I looked in the altcdfenvs package and it looks as if I could hijack another env and change the parameters as needed. Has anyone done this? Is there a tutorial or Vignette I overlooked? Is there another tool for building cdf files? thanks Nicholas
altcdfenvs • 432 views
ADD COMMENTlink modified 13.6 years ago by lgautier@altern.org950 • written 13.6 years ago by Nicholas Lewin-Koh430
Answer: Creating a CDFenv without cdf file
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gravatar for lgautier@altern.org
13.6 years ago by
lgautier@altern.org950 wrote:
> Hi, > I have many cel files from a custom chip, but I do not have the cdf file. I do have the chip design information and > and the seqence information but they are in seperate text files. I looked in the altcdfenvs package and it looks > as if I could hijack another env and change the parameters as needed. Has anyone done this? Well, building you cdfenv from scratch would be easier I think. The package altcdfenvs proposes a class to wrap cdfenvs and convenience methods to slice, dice, and do basic sanity checks on that beast. Once I hoped that this class, or actually a class, would make it to the rest of "affy" and "makecdfenv", but apparently it did not. You can use the class when building your thing then extract the environment from its slot when done, or go directly with an environment. > Is there a tutorial > or Vignette I overlooked? No tutorial for this exact sequence of steps, but looking at the code that makes cdfenvs from the results of matchprobes in altcdfenvs should help you to write your own. In short, you will want something like: - read through your 'design files' and get for each probe its location (X/Y coordinates) and the probeset it belongs to. | -- resolve each X/Y pair of coordinates to an 'index' (that is the row index for the probe level data in the AffyBatch object) using the function xy2indice (note that you will need the geometry for your chip -number of rows/number of cols-... if you do not have it, try to take the square root of the number of probe-level values in your cell file: Affymetrix chips are often squares). | -- populate your cdfenv environment with keys that are probeset identifiers ("12345_at"-like strings) and values that are two-columns matrices (first column being PM, second column being MM... if nothing is known about MMs and no plan to use them set them all to NA, otherwise there is a dangerous empirical rule saying that MMs are next to their respective PM). > Is there another tool for building cdf files? None that I know of... may be the interface to the affymetrix readers/parsers ? Hoping this helps, L. > thanks > Nicholas > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 13.6 years ago by lgautier@altern.org950
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