I can't see to find a cdf file for the new array from Affymetrix, Clariom S Human HT. Can anyone guide me as to where to obtain one?
It's not clear what you are asking for. If you want the actual cdf file from Affymetrix, then it doesn't exist, so far as I know (and this isn't the place to ask for that - we are not Affymetrix). If you are asking for the cdf package, then that doesn't exist either, as A) there isn't a cdf file for this array and B) the makecdfenv/affy analysis pipeline doesn't support this array type.
What does support this array type is the oligo package, which will automatically install the pd.clariom.s.human package, which does pretty much the same thing that the old cdf packages did.
great thanks, I found your previous post using oligo and the db file. Thanks for your guidance.
Kathleen
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version 2.3.6
But do note that gcrma doesn't support this array either, as it doesn't have MM probes, really, and as already mentioned, the makecdfenv/affy pipeline doesn't support this array type, so by definition neither does gcrma.
The correct question would have been, in the limma manual they suggest to use gcrma which does not seem to support the Affymetrix Clariom S Human HT array. Which package would you suggest for reading and normalizing this array. Perhaps someone could suggest the update to the limma manual.