Question: How can I use the information from an ADF [Array Design File] file for microarray normalization?
6.9 years ago by
Christoph Geisenberger • 10 wrote:
Hi, I am currently analyzing the expression data from Glioblastoma samples provided by the TCGA. As an additional validation data set I downloaded a collection of Affymetrix cel files. For better comparability I would like to use the same probeset mapping as TCGA did for their chips. For this purpose, a so called ADF [array description file] is supplied (https://tcga-data.nci.nih.gov/tcga/tcgaPlatformDesign.jsp). It contains the probeset ID, the chromosomal location and the NCBI gene ID. I have previously used costum CDF files for the normalization of Affy cel files. I am now wondering how I can use the information from the ADF file for the normalization process. Do I have to convert the ADF file to a CDF file first? Or is there some way to re-map a already available CDF file? Thank you very much, Christoph [[alternative HTML version deleted]]
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