Table 1 Description of three ACs for comparing data generated from the Affymetrix platform with data generated from the Agilent platform and three methods to identify the CT sets between two platforms

From: Consistency of predictive signature genes and classifiers generated using different microarray platforms

Abbreviation

Description

AC

 AC 1

The intensity data of the Affymetrix microarrays (418 samples) compares with the averaged ratio data from the dye-swapped Agilent microarrays (318 samples).

AC 2

The ratio data of the Affymetrix microarrays (318 samples) compares with the averaged ratio data from the dye-swapped Agilent microarrays (318 samples).a

AC 3

The intensity data of the Affymetrix microarrays (318 samples) compares with the intensity data extracted from the Agilent platform (318 samples).b

CT

 SeqMap

The most stringent method employed a sequence-based mapping approach (4860 CTs).c

 RefSeq

The less stringent method was to identify the probes/probesets from both platforms having the same RefSeq ID (6312 CTs).

 Unigene

The least stringent approach was used to generate the list of Unigene-based CTs (9954 CTs).

  1. Abbreviations: AC, analysis configuration; CT, common transcript; MAQC, MicroArray Quality Control Phase.
  2. aThe Affymetrix ratio data were calculated using its intensity data similar to the ratios produced by ‘dual’ samples assayed on the Agilent platform (a treated sample compared to an average of the corresponding control samples).
  3. bIn the first phase of the MAQC project, a comparative analysis between one-color and two-color data generated on the same platform revealed that the intensity value from the single channel of the two-color array exhibits similar sensitivity/specificity as the two-color ratio array data.18 Therefore, the intensity data are the average value of Cy3 and Cy5 corresponding only to the treated samples.
  4. cThe method is identical to the one used in the MAQC-I project.19
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