[BioC] GeneAnswer package Query

Steve Lianoglou mailinglist.honeypot at gmail.com
Sat Sep 1 17:20:48 CEST 2012

Hi Reema,

On Sat, Sep 1, 2012 at 11:11 AM, Reema Singh <reema28sep at gmail.com> wrote:
> Dear all
> I am getting following error, when try to get network graph using
> GeneAnswer package
>> geneAnswersConceptNet(xx, colorValueColumn='foldChange',
> centroidSize='pvalue', output='interactive')
>  Error in `*tmp*`[[4]] : subscript out of bounds
> Any suggestion would be a great help.

You'd need to give us some reproducible example to help us to help you
best ... for instance, what's in `xx`? Is it a matrix? data.frame?
list? something else?

You might be able to start to help yourself by calling `traceback()`
after the error is fired to see where inside the
`geneAnswersConceptNet` the error occurs -- this will also require you
to start looking at the code of the `geneAnswersConceptNet` function
to see why you are missing some expected index (which is always a good
idea to do when you get such problems, anyway).


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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