How To Generate A New Cdf File ?

Question

[Mycroft34]

Hello,

I have got a list of probes that I would like to mask out from future analysis of expression using a HGU133plus2 affymetrix chip.

I have read that I should modify the corresponding cdf file.

Is that correct ?

And how could I do that from R and Bioconductor ?

Finally, is the resulting cdf file directly usable in future analyses ?

Thanks for any help.

Answer 1

[Maxime Lamontagne]

You could check makecdfenv from Bioconductor, but I don't understand why you want to modify your cvf file to exclude probeset. You should remove probeset after transforming your cel files in txt file with Affymetrix Power Tools.

[Mycroft34]

Someone in the lab is working on human xenogrefs in mouse, and wants to check expression of genes in the transplanted human cells. He asked me to find all the human probes from the affymetrix chip that are matching mouse transcripts. I got that list of probes and probesets, and liked to have a file selecting human specific probes. Something similar to what Naef et al. did in Nuc. Acids Res. (2005) vol.33 e111. They used their modified list of probes by modifying cdf files. Is there another easiest mean to do that ?

[Maxime Lamontagne]

Personally, I would use Affymetrix Power Tools to generate the rma.summary.txt file. After, you could extract your probeset from this file by using R.

[Mycroft34]

Thanks; I'll try that.

[Neilfws]

I agree; it's much easier to filter probes after processing CEL files than to try messing around with custom CDF files.