[BioC] averaging multiple probes for same gene on agilent array

[Alison Waller]

Dear Bioconductor list,

I am analysing data from  a custom Agilent array with 3600 spots using  
Limma.

There are 3 probes for each gene (usually, however some genes only  
have one probe), all probes are in duplicate.

I would like to obtain an average M value for each gene.

Examples of the spot ID's are as below.
D137-cbdb_A1587_1
D137-cbdb_A1587_1
D137-cbdb_A1587_2
D137-cbdb_A1587_2
D137-cbdb_A1587_3
D137-cbdb_A1587_3
D138-cbdb_A1594
D138-cbdb_A1594


One option I thought of was to adjust the GAL file to have identical  
IDs for all of the probes for the same gene and then use the avereps()  
function.

ID	Name

D137	D137-cbdb_A1587_1
D137	D137-cbdb_A1587_1
D137	D137-cbdb_A1587_2
D137	D137-cbdb_A1587_2
D137	D137-cbdb_A1587_3
D137	D137-cbdb_A1587_3
D138	D138-cbdb_A1594
D138	D138-cbdb_A1594

However, the avereps() function seems more suitable for actual  
duplicates, for probesets I would like to use some weighted average  
where probes with intensities which are futher from the mean of the  
probe set are down weighted (for example the tukey biweight).

Does anyone have experience with similar arrays or suggestions of an  
appropriate function.

thank you,

alison

---------------------------------------------------------
Alison Waller  Ph.D
alison.waller at utoronto.ca