[BioC] GeneAnswer package Query

[Gang Feng]

Hi, Reema

Please give us more info, like Steve and Sean stated in their previous
responses.

Basically, for geneAnswersConceptNet(), xx should be an instance of
GeneAnswers. So you can run
> class(xx)

If the output is not like this,

[1] "GeneAnswers"
attr(,"package")
[1] "GeneAnswers"


You need geneAnswersBuilder() to build a GeneAnswers instance at first.

There is one thing that you might need to know. Because of a large update
(especially index change) of igraph, which is one of GeneAnswers dependent
packages, the current version, 0.6.x does NOT work with GeneAnswers. The
developer of igraph provides a temp solution, igraph0, an old version of
igraph. So each time, when you launch R and GeneAnswers WITHOUT starting
the latest igraph, the current GeneAnswers is fine. But once you launch
the new igraph, all of network related functions won't work. We are
working on this issue right now and hope that the new version GeneAnswers
in OCT will work with the new igraph and Reactome.db .

Thanks

Gilbert


BTW, does anyone know how I can directly reply the original thread in
daily digest? I searched online, but didn't get any clue. Thanks a lot!

On 9/2/12 5:00 AM, "bioconductor-request at r-project.org"
<bioconductor-request at r-project.org> wrote:

>   8. GeneAnswer package Query (Reema Singh)
>   9. Re: GeneAnswer package Query (Steve Lianoglou)
>  10. Re: GeneAnswer package Query (Sean Davis)
>
>
>------------------------------
>
>Message: 8
>Date: Sat, 1 Sep 2012 20:41:46 +0530
>From: Reema Singh <reema28sep at gmail.com>
>To: bioconductor <bioconductor at r-project.org>
>Subject: [BioC] GeneAnswer package Query
>Message-ID:
>	<CAEHmZ4uDWoubcLHMzCbecvn4047N9_JhRqDjYNAYM+0TEpAgkA at mail.gmail.com>
>Content-Type: text/plain
>
>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.
>
>Regards
>Reema Singh
>
>	[[alternative HTML version deleted]]
>
>
>
>------------------------------
>
>Message: 9
>Date: Sat, 1 Sep 2012 11:20:48 -0400
>From: Steve Lianoglou <mailinglist.honeypot at gmail.com>
>To: Reema Singh <reema28sep at gmail.com>
>Cc: bioconductor <bioconductor at r-project.org>
>Subject: Re: [BioC] GeneAnswer package Query
>Message-ID:
>	<CAHA9McNi2wvTtvEegB2g3=8xQ7_fgBVpbB_OjJSoE8Gf8zg9Gw at mail.gmail.com>
>Content-Type: text/plain; charset=ISO-8859-1
>
>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).
>
>HTH,
>-steve
>
>-- 
>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
>
>
>
>------------------------------
>
>Message: 10
>Date: Sat, 1 Sep 2012 11:23:46 -0400
>From: Sean Davis <sdavis2 at mail.nih.gov>
>To: Steve Lianoglou <mailinglist.honeypot at gmail.com>
>Cc: bioconductor <bioconductor at r-project.org>
>Subject: Re: [BioC] GeneAnswer package Query
>Message-ID:
>	<CANeAVBkL2hOoKmv5V2z5rV1NpWfniZOLryWoKRfJeC04kFhS-w at mail.gmail.com>
>Content-Type: text/plain
>
>On Sat, Sep 1, 2012 at 11:20 AM, Steve Lianoglou <
>mailinglist.honeypot at gmail.com> wrote:
>
>> 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).
>>
>>
>And don't forget to include sessionInfo().
>
>Sean
>
>	[[alternative HTML version deleted]]