Description Usage Arguments Details Author(s) See Also Examples

Calculates the splicing index for the probesets in one or more genes, as defined in the Affymetrix white paper "Alternative Transcript Analysis Methods for Exon Arrays".

1 2 | ```
spliceGroupIndex( x, group.column, members )
spliceIndex( x, ids, group, gps, group.index.fn=spliceGroupIndex, median.gene=FALSE, median.probeset=FALSE, unlogged=TRUE )
``` |

`x` |
eSet containing expression data |

`group.column` |
a column name for the group data |

`members` |
a set of arrays |

`ids` |
Character vector of Ensembl gene names |

`group` |
If defined, the column name in the ExpressionSet's pData object in which to look for gps |

`gps` |
The two sets of arrays to compare |

`group.index.fn` |
a method which, when passed an ExpressionSet (from the Biobase package), a column name for the group data and a set of arrays, will return the indices of interest |

`median.gene` |
Use the median instead of the mean when calculating averages across genes |

`median.probeset` |
Use the median instead of the mean when calculating averages across probesets in each replicate group |

`unlogged` |
Unlog the expression data before calculating the splicing index (and then re-log afterwards) |

The splicing index gives a measure of the difference in expression level for each probeset
in a gene between two sets of arrays, relative to the gene-level average in each set. This
is calculated only for those probesets that are defined as exonic (See `exonic`

).

The two sets of arrays can be specified in two ways: First, by using numeric indices defining the appropriate columns in the expression data. This is done by supplying these as a list to gps (e.g. gps=list(1:3,4:6) will calculate the splicing index between arrays 1,2,3 and 4,5,6. Alternatively, the annotation in the phenoData object from x can be used (e.g. group="treatment",gps=c("a","b") will compare between the arrays labelled 'a', and 'b' in the 'treatment' column of pData(x)).

The implementation also calculates a p.value and t.statistic for each probeset; these are returned alongside the splicing index.

By default, the splicing index is calculated using the mean across genes and samples. Specifying median.gene=TRUE or median.probeset=TRUE will use the median instead (for the gene or probeset level averages, respectively). It is calculated using the unlogged data, unless unlogged=FALSE. This only affects the internal calculations; values in x are always assumed to be logged, and the splicing index is always returned on the log2 scale.

Tim Yates Crispin J. Miller

1 2 3 4 5 | ```
if(interactive()) {
# Loads the Expression Set into x.rma
load( '../unitTests/HuEx-1_0.tp53.expr.RData' )
spliceIndex( x.rma, symbolToGene( 'tp53' ), gps=list(1:3,4:6) )
}
``` |

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