Dear All

 

Having given a training course in this area earlier this year, I thought
I would contribute some sample code on how to visualise microarray data
on KEGG pathways using KEGGSOAP.

 

This can be found by going to our webpage
(http://www.iah.ac.uk/research/bioinformatics/bioinf.shtml)  and
clicking on "Sample Code".

 

The code is in three sections.  The first simply uses GEOquery and
biomaRt to retrieve some Affymetrix array data from GEO and link it to
ensembl id using Biomart.  NOTE: I sometimes have trouble getting the
data from the NCBI servers, and if this step fails, none of the
subsequent code will work - please be patient.   The second section then
downloads some files from the KEGG ftp server, and uses the merge()
function to link the array data to the relevant pathways.  Finally, the
third section uses KEGGSOAP and geneplotter to colour KEGG pathways
according to the array values.

 

The code is freely available without guarantee or warranty!  Do whatever
you like with it, but I would appreciate an acknowledgement in whatever
you do.

 

Thanks

Mick

 

Head of Bioinformatics
Institute for Animal Health
Compton
Berks
RG20 7NN
01635 578411 

 

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