I am currently attempting to analyze some Affymetrix Whole Transcript Expression data using JMP Genomics 5.0. My data was generated using the Affymetrix Mouse Gene 1.1 ST Array. My dataset consists of 2 array plates for a total of 192 samples. No matter how many of those samples I try to analyze (I've tried 3, 10, 96, or 192) I keep getting the ERROR message below.
"ERROR: There is no available output dataset after the probe filter. finished with AfterDataParse"
"ERROR: AffymetrixWholeTXInputEngine exited due to errors."
I'm not sure exactly sure how to trouble shoot this problem on my own, so I would be open to any suggestions.