[BioC] SPIA - changes between 1.4.0 and 1.60.
lavinia.gordon at mcri.edu.au
Tue Sep 14 01:13:48 CEST 2010
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.
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
Senior Bioinformatics Officer
Murdoch Childrens Research Institute
Royal Children's Hospital
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