GUS Schema >> RAD::AffymetrixMAS4 (subclass of RAD::CompositeElementResult )

This view of CompositeElementResultImp is for quantification of microarray data using Affymetrix Microarray Suite, Version 4.0.

Light yellow rows indicate columns provided from the superclass.

column nulls? type description
COMPOSITE_ELEMENT_RESULT_ID no NUMBER(10,0) primary key Edit
SUBCLASS_VIEW no STRING(27) Edit
COMPOSITE_ELEMENT_ID no RAD::CompositeElement (NUMBER(10,0) )FK to CompositeElement, the corresponding entry in the composite element view this result is referring to. Edit
QUANTIFICATION_ID no RAD::Quantification (NUMBER(8,0) )FK to quantification. There can be CompositeElementResult values without corresponding ElementResult's, as can be the case in summary values for Affy probe sets. Edit
POSITIVE_PROBE_PAIRS NUMBER(3,0) The number of probe pairs where the intensity of the perfect match (PM) is significantly greater than the corresponding intensity of the mismatch (MM). Edit
NEGATIVE_PROBE_PAIRS NUMBER(3,0) The number of probe pairs where the intensity of the mismatch (MM) is significantly greater than the corresponding intensity of the perfect match (PM). Edit
NUM_PROBE_PAIRS_USED NUMBER(3,0) Pairs used = total probe pairs per probe set - (probe pairs masked in a mask file) - (probe pairs masked in the image). Edit
PAIRS_IN_AVERAGE NUMBER(5,0) A trimmed probe set that excludes probes with extremely intense or weak signal from the analysis. Edit
LOG_AVERAGE_RATIO FLOATThe log of the PM/MM ratio is calculated for each probe pair in a probe set. The average is then taken across the pairs_in_average. This is a measure of the strength of the hybridization. A greater log average indicates an increased likelihood of the presence of that transcript. Edit
AVERAGE_DIFFERENCE FLOATThe average difference is a measure of the relative expression of a transcript and can be used to compare expression across experiments. It is calculated by taking the average of the difference between the PM - MM of each probe pair in the pairs_in_average (after excluding extreme values as described for pairs_in_average). Edit
ABSOLUTE_CALL STRING(500) A categorical statement about the likelihood of the presence of a transcript. The calls are: present (P), Marginal (M), or Absent (A). The call is made by a weight matrix which takes the following into consideration: the ratio of positive to negative probe pairs, the positive fraction (the number of positive probe pairs / the nuber of probe pairs used), and the log average ratio. Edit

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