Class GeoConverterMoleculeTest

java.lang.Object
ubic.gemma.core.loader.expression.geo.GeoConverterMoleculeTest
public class GeoConverterMoleculeTest extends Object
Which channel's molecule describes the SAMPLE.
Author:
gembro

  • Constructor Details

    • GeoConverterMoleculeTest

      public GeoConverterMoleculeTest()

  • Method Details

    • testNoChannelReportsAMolecule

      @Test public void testNoChannelReportsAMolecule()

    • testChannelsAgreeing

      @Test public void testChannelsAgreeing()

    • testGenomicDnaIsAReferenceChannelAndNotTheSample

      @Test public void testGenomicDnaIsAReferenceChannelAndNotTheSample()
      🛑 The GSE9164 case. A two-colour sample co-hybridized against a genomic-DNA reference disagrees by construction, and only the non-DNA channel is the sample. Taking channel 1 by position labelled all 14 of its assays genomicDNA on prod while every description read "Total RNA ... RNeasy Mini Kit"; GEO's GSM230264 has ch1 genomic DNA (Cy3) and ch2 total RNA (Cy5).

      Order must not matter — the reference is not reliably first.

    • testTwoRnaFlavoursStayUnset

      @Test public void testTwoRnaFlavoursStayUnset()
      ...but only genomic DNA earns that treatment. Two RNA flavours name no reference, so nothing distinguishes them and asserting either would claim GEO said something it did not.

    • testThreeMoleculesStayUnset

      @Test public void testThreeMoleculesStayUnset()
      Three disagreeing channels are not the two-colour shape either, DNA present or not.