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

`exonic`

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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