Thursday, October 28, 2010

GeneChip® Mouse Expression Set 430

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What is a probe set? What do the different suffixes attached to a probe set name mean?
A probe set is a collection of probes designed to interrogate a given sequence. A probe set name is used to refer to a probe set, which looks like the following:
12345_at or 12345_a_at or 12345_s_at or 12345_x_at
The last three characters (_at, in RED) identify the probe set strand. Probe sets that are designed to detect the anti-sense strand of the gene of interest are annotated with "_at".
There are different types of probe sets that can result from the probe selection process. Most probe sets have an extension of an underscore and a letter to designate the probe set type, except for unique probe sets. These different probe set types are shown in the example above in BLUE.
Probes in a gene family probe set (_a set) all cross-hybridize to the same set of sequences that belong to the same gene family (i.e. having same name in the "geneCluster" column). This probe set type is only created if the "geneCluster" column is included in the Instruction File and contains information.
Probes in a unique probe set do not cross-hybridize to any other sequences in the design (including any additional pruning sequences provided).
Probes in an identical probe set (_s set) all cross-hybridize to the same set of sequences that are used for the design (including any additional pruning sequences if provided). These sequences are not defined as from the same gene family for one the following reasons: the values in the "geneCluster" column are different, or the gene family information is not provided.
Probes in a mixed probe set (_x set) contain at least one probe that cross-hybridizes with other sequence(s) used for the design. Cross-hybridizing probes have a cross-hybridization penalty applied to their raw probe scores, and thus, favoring unique probes of the same quality over cross-hybridizing probes.
The following diagram is a graphical representation of these different probe set types.

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