Hi I am trying to analyze HTA 2.0 data with the aroma.affymetrix package. This data is said to contain junction probes which are present in the CDF file on the exon level. However, when I perform a background correction, a normalization and extract the data, the junction probes do not seem to be present anymore. Is this something someone has encountered before? Might the reason be that the probeset ids for these junction are form a different format than the other ones? Or am I missing something in my extracted data?
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