GeneChip™ Human Genome U133A 2.0 Array

The intended use of the 100 probe sets is to allow users to normalize data across the chip. These 100 probe sets are considered normalization controls. They were found to have consistent levels of expression across multiple tissue types and treatments.

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Occasionally, it is not possible to select either a unique probe set or a probe set with all probes common among multiple transcripts ("_s_at" ). In such cases, similarity criteria are suspended, and the resulting probe set name is appended with the "_x_at" extension. These probe sets contain some probes that are identical, or highly similar, to unrelated sequences. These probes may cross-hybridize in an unpredictable manner with sequences other than the main target. Data generated from these probe sets should be interpreted with caution, due to the likelihood that some of the signal is from transcripts other than the one being intentionally measured.

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The primary goal in probe set selection is to select a probe set unique to a single transcript or common among a small set of similar transcript variants. A probe set name is appended with the "_s_at" extension when all the probes exactly match multiple transcripts. The probe set selection process generally favors probe sets measuring fewer transcripts. Probe sets with common probes among multiple transcripts (the "_s_at" probe sets), are frequent and are to be expected, due to alternative polyadenylation and alternative splicing. In most cases, "_s_at" probe sets represent transcripts from the same gene, but the same probe set can sometimes also represent transcripts from homologous genes. One transcript may be represented by both a unique and an "_s_at" probe set when the transcript variation is sufficient.

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There are two ways to export the CEL file from GCOS v1.4 as a text file.

1. In GCOS 1.4 use GCOS Manager to navigate to the CEL file in the process database. Highlight the CEL file and right click to export the data from the process tab. You may want to change the data location where the export will be stored before you start.
2. In GCOS 1.4 use the find feature in GCOS Manager to find the CEL files and export those selected as a text file. This approach allows export of more than one experiment at a time.

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Command Console cannot generate a comparison analysis between different array types.

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