[BioC] Using probes2table without affy probeset IDs

James W. MacDonald jmacdon at med.umich.edu
Fri Aug 15 15:37:40 CEST 2008

Hi Ingileif,

Ingileif B. Hallgrimsdottir wrote:
> Hi,
> I have analysed my affy data using an alternative cdf-file 
> (hs133phsense) and would like to obtain an html-table summarizing the 
> results, similar to the output of probes2table.  Is there a way to use 
> probes2table even when the input is not a list of affy probeset names?  
> Are there other functions available, similar to probes2table?

Yes, you can use probes2tableBM() which uses biomaRt for the lookup 
rather than the annotation package. The function arguments are quite 
similar to probes2table(), but there are some differences, so please see 
the help page for more info.

If you really like the annaffy-style HTML with the green colors on the 
expression values you could alternatively use the SQLForge functions 
inside of AnnotationDbi package to build your own annotation.db package 
which you could then use with probes2table.



> Many thanks,
> Ingileif Hallgrimsdottir
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James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646

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