[BioC] coerce aafTable object into dataframe (annaffy)

[Georg Otto]

"Colin A. Smith" <colin at colinsmith.org> writes:
Colin,

>> So the question arises:
>> Is there a way to merge aafTables of different sizes?
>
> Now there is. I implemented the all, all.x, and all.y options in  
> annaffy's merge function. Before I commit the change, it would be  
> great if you could test out the modified function to see if it will  
> work for you. Download the following and source it into your R  
> session after loading annaffy:
>
> http://zinc.compbio.ucsf.edu/~colin/merge.aafTable.R
>

Thanks a lot!

> anntable.merged <- merge(anntable.affy, anntable.tigr, all = TRUE)

works exactly the way I need it.

There is one more (and hopefully last) question I have concerning
reading data into aafTable objects (sorry for this, but my knowledge
concerning these kind of data structures is still somewhat limited,
and I haven't found anything about it):

Some annotation tables (eg. output from biomaRt) have multiple
annotations per probeset ID, that is represented in the table as
multiple rows, e.g.

Probeset        Ensembl ID
A               1
A               2
A               3
A               4
B               5
B               6
C               7


Is there a way I could write this in an aafTable in the same way as it
is done in the affy annotation packages, i.e. with multiple
annotations per field, something like this:

anntable at probeids      anntable at table$"Ensembl ID"
A                      1 2 3 4
B                      5 6
C                      7

Any hint will be highly appreciated.

Cheers and thanks again,

Georg