Hmm... this looks weird but as usual, there's probably a simple
explanation to it. Yes, it could possibly be that the CDF is
incompatible with the CEL files, but in that case I'd expect an
informative error message explaining why.
In a fresh R session, what does the following output?
library("aroma.affymetrix")
cdf <- AffymetrixCdfFile$byChipType("hjay", tags="r1,TC")
cs <- AffymetrixCelSet$byName("Data_Study1", cdf=cdf, verbose=-100)
The output is quite long, but it'll help me/you troubleshoot.
Also, what's the output of sessionInfo() after the above?
/Henrik
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