Question: Affymetrix Human Gene 1.0 ST Array
11.5 years ago by
Hans-Ulrich Klein • 330
Hans-Ulrich Klein • 330 wrote:
Dear List, I would like to analyze Hume Gene 1.0 ST Arrays using BioC. I am interested in differential expression at probeset and at gene level. Searching the list archives reveals, that "makecdfenv and makePlatformDesign make the assumption that there is a one-to-one mapping of probe ==> probeset", which is not true for the Human Gene 1.0 chip. Anyway, I found some interesting packages: - exonmap: Looks promising, but there are no cdf files for the Gene 1.0 Chip on the related website (just for the Exon 1.0) - xps: This seems to be a completely new infrastructure for affymetrix chips, which is capable of reading the Gene 1.0 Chip. - aroma.affymetrix: This is not a BioC package. (Why not?) Have I overseen a package? Can someone point me to further information regarding BioC and the Human Gene Chip? I am not sure where to start and appreciate any comments and experiences of other users. Best wishes, Hans-Ulrich PS: Is there any work going on the integration the Human / Exon Chip in the affy packages? Or are these Chips too different from the conventional 3' Chips.
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