[BioC] Conversion of affymetrix annotation environment to matrix

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Fri Mar 10 15:52:59 CET 2006


Hi

I want to convert the drosgenome1GO environment to a matrix with
columns:

Affy-probe_id, GOID, GOEvidence, GOOntology

I have figured out that if I do:

lis <- as.list(drosgenome1GO)
lis2 <- lis[!is.na(lis)]
m <- matrix(unlist(lis2), ncol=3, byrow=TRUE)

I get something approaching what I want (ie a matrix with columns GO ID,
GO Evidence and GO Ontology), but I also want the actual affy probe ids
in there as a column (I eventually want to do a table join from the
output of topTable() to this table)

Thanks
Mick



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