[BioC] SPIA - changes between 1.4.0 and 1.60.
sorin at wayne.edu
Tue Sep 14 01:17:11 CEST 2010
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.
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
> 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.
>> 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
>> -----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
>> Victoria 3052
Director of the Intelligent Systems and Bioinformatics Laboratory
Department of Computer Science
Wayne State University
Room 431 State Hall,
5143 Cass Ave,
Detroit, MI 48202
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