Class RealDesignsFitTest

java.lang.Object
ubic.gemma.core.util.math.linearmodels.RealDesignsFitTest
public class RealDesignsFitTest extends Object
Paired / repeated-measures fits against limma on REAL Gemma designs, one fixture per design shape (see data/stat-tests/real-designs/fetch_real_designs.py for how each was chosen, and real-designs-golden-gen.R for the reference fits; the golden values are read from each golden.txt, not copied here).
  • GSE33658: 11 patients x 2, balanced pairs
  • GSE7400: 5 pairs, 4 residual dof
  • GSE95298: 20 cell lines, block sizes 2 and 4, rho near its upper clamp (0.978)
  • GSE246769: 8 subjects, 3-4 samples each, a four-level within-subject factor
  • GSE32473: 10 patients x 3 arms, a three-level within-subject factor, rho 0.83
  • GSE63857: RNA-seq with a singleton block among blocks of 2 and 4
  • GSE137: 35 x 2 with no recorded condition (intercept-only design plus block)
  • GSE55468: every individual measured once (no repeated measures)

  • Constructor Details

    • RealDesignsFitTest

      public RealDesignsFitTest()