[BioC] SPIA - changes between 1.4.0 and 1.60.

[Lavinia Gordon]

  Hi Sorin,
Yes Adi's email does answer my question.
thanks

Lavinia.

On 14/09/2010 9:52 AM, Sorin Draghici wrote:
> Lavinia,
>
> I'm not sure whether you are interested in how the software was changed or how
> those changes were documented.
>
> For the former, as Adi said in his previous email, the first version ignored
> nodes in the KEGG pathway that were associated with several genes.
>
> For the latter, the link you included shows this for SPIA:
> "updated pathway data by including interactions between genes and KEGG groups
> that contain at least one gene"
>
> Does this answer your question ?
>
> Sorin
>
>
>
>
> On 9/13/2010 7:43 PM, Lavinia Gordon wrote:
>>   Hi Sorin,
>>
>> thank you for your email.
>> So to rephrase my question slightly, where does it say that nodes and links
>> previously ignored are now considered in the analysis, comparing version 1.6 to
>> 1.4?  The only document that I have found is here:
>> http://fgc.lsi.umich.edu/cgi-bin/blosxom.cgi/2009/10/13
>> which is no longer updated.
>> If I look at the KEGG updates (http://www.genome.jp/kegg/docs/relnote.html), it
>> would appear to suggest that no major changes have occurred in between the two
>> SPIA versions.
>>
>> with regards
>>
>> Lavinia.
>>
>> On 14/09/2010 9:17 AM, Sorin Draghici wrote:
>>> Lavinia,
>>>
>>> The results are bound to be different because now: i) the KEGG pathways
>>> themselves are different and ii) nodes and links previously ignored are now
>>> considered in the analysis.
>>>
>>> Regards,
>>>
>>> Sorin
>>>
>>>
>>>
>>> On 9/13/2010 7:13 PM, Lavinia Gordon wrote:
>>>>    Hi Adi,
>>>>
>>>> Thank you for your answer, that is very helpful.
>>>> Is there any document/site that indicates these changes?  I have seen changelogs
>>>> before but wasn't able to find anything for SPIA.  The reason that I ask is that
>>>> I have just re-run some old code and have quite different SPIA results between
>>>> the old and new version.
>>>> Thank you for your efforts in putting together this package.  It is extremely
>>>> user-friendly and has generated some very nice results.
>>>>
>>>> with regards
>>>>
>>>> Lavinia.
>>>>
>>>> On 14/09/2010 1:02 AM, Tarca, Adi wrote:
>>>>> Hi Lavinia,
>>>>> This is a good question and I think other users would benefit from reading the
>>>>> answer. Therefore it would be useful if you send your questions to the
>>>>> bioconductor mailing list also.
>>>>> I will give you the answer now anyhow.
>>>>>
>>>>> The main change from SPIA 1.4.0 to 1.6.0 is the KEGG pathway data on which
>>>>> SPIA works. KEGG pathways are updated periodically (genes are removed or
>>>>> added, connections apear or are removed). In addition to this we also changed
>>>>> the way we parse those raw pathway data. Initially only links between gene
>>>>> type of nodes were considered. Now we consider also links between "group"
>>>>> types of objects that include one or more genes.
>>>>>
>>>>> Regards,
>>>>> Adi
>>>>>
>>>>>
>>>>> Adi Laurentiu Tarca, PhD
>>>>> Assistant Professor (Research),
>>>>> Department of Computer Science&    Center for Molecular Medicine and Genetics,
>>>>> Wayne State University,
>>>>> 3990 John R., Office 4809,
>>>>> Detroit, Michigan 48201
>>>>> Tel: 1-313-5775305
>>>>> http://bioinformaticsprb.med.wayne.edu/tarca
>>>>>
>>>>> -----Original Message-----
>>>>> From: Lavinia Gordon [mailto:lavinia.gordon at mcri.edu.au]
>>>>> Sent: Sunday, September 12, 2010 10:58 PM
>>>>> To: Tarca, Adi
>>>>> Subject: SPIA - changes between 1.4.0 and 1.60.
>>>>>
>>>>>      Dear Dr Tarca,
>>>>>
>>>>> My apologies for the simple question, as I am sure that this information must
>>>>> be available, (at Bioconductor?), but I cannot find it.  I just wondered what
>>>>> the changes were to the SPIA package between version 1.4.0 and 1.6.0?
>>>>>
>>>>> with many thanks for your time,
>>>>>
>>>>> Lavinia Gordon.
>>>>>
>>>>> -- 
>>>>> Senior Bioinformatics Officer
>>>>> Murdoch Childrens Research Institute
>>>>> Royal Children's Hospital
>>>>> Flemington Road
>>>>> Parkville
>>>>> Victoria 3052
>>>>> Australia
>>>>> www.mcri.edu.au
>>>>>
>>>>>
>>


-- 
Senior Bioinformatics Officer
Murdoch Childrens Research Institute
Royal Children's Hospital
Flemington Road
Parkville
Victoria 3052
Australia
www.mcri.edu.au