[BioC] affylmGUI

Simon Kidd kidd at mail.rockefeller.edu
Tue May 11 19:00:07 CEST 2004


We have affylmGUI running on Mac OSX and R2 dev. A couple of things 
seem not to work. We can save all the plots except for venn diagrams 
where we get an error message saying:

Error in paste(limmaDataSetNmaeText, "VennDiagram", sep = "") : 
Object "limmaDataSetNameText" not found

When we try to do a Heat diagram we get this error message:

Error in try(expr, TRUE): No loop to break from, jumping to top level

followed by a second error message:

Cannot find package drosgenome1

(ours are Drosophila chips and the drosgenome1 package is installed 
in /users/me/Library/R/library/drosgenome1cdf)

There are then a bunch of related messages to not finding drosgenome1

In the end we end up with a black heat diagram.

Perhaps, related to this when we try to use gene symbols instead of 
probe ids we get this error message:

Error in "[.data.frame"(genelist, topGenes, IDorSymbol) : undefined 
columns selected

What P value is used to define significant in the venn diagram?



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