R help - Aug 2008 - similarity between two gene lists with varied length

Dear listers,

a little off-topic:

I am looking for and compare algorithms which can calculate "distance"
or
"similarity" between two gene lists with different lengths.

Any paper, any implementation in R and any suggestion is welcome!

Thanks,

-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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Actually, making this question more nontrivial is, 1. the lengths for the
two gene lists are very different; 2. I could add another list as gene
weight to any gene, for example, of union of two gene lists.

On Sun, Aug 24, 2008 at 9:15 AM, Shannon, William
<WSHANNON@dom.wustl.edu>wrote:
> First thought is a similarity can be based on the ratio of the number of
> genes in the intersection of the two lists divided by the number of genes
in
> the union of the two lists.  If the two lists are identical the similarity
> is 1 and if they have no genes in common they have a similarity of 0.  Of
> course this won't take into account the length of the gene lists.
>
> You would have to think through what would happen to the similarity for
> cases where some genes are in both lists.
>
>
> Bill Shannon
> Associate Professor of Biostatistics in Medicine
> Washington University School of Medicine
>
> President-Elect, Classification Society
>
> ________________________________________
> From: bioconductor-bounces@stat.math.ethz.ch [
> bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Weiwei Shi [
> helprhelp@gmail.com]
> Sent: Saturday, August 23, 2008 7:55 PM
> To: r-help@stat.math.ethz.ch
> Cc: Bioconductor
> Subject: [BioC] similarity between two gene lists with varied length
>
> Dear listers,
>
> a little off-topic:
>
> I am looking for and compare algorithms which can calculate
"distance" or
> "similarity" between two gene lists with different lengths.
>
> Any paper, any implementation in R and any suggestion is welcome!
>
> Thanks,
>
> --
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
>
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>


-- 
Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

	[[alternative HTML version deleted]]

Hi, Weiwei,

I think you can try fisher exact test simply. Take all genes of your
organism as sample pool and your question is that: when you selected two
gene lists from the sample pool, how to judge the independence of the two
gene lists. The fisher exact test worked for this type of question.

Best wishes,

Weibo

On Sun, Aug 24, 2008 at 8:55 AM, Weiwei Shi <helprhelp@gmail.com> wrote:
> Dear listers,
>
> a little off-topic:
>
> I am looking for and compare algorithms which can calculate
"distance" or
> "similarity" between two gene lists with different lengths.
>
> Any paper, any implementation in R and any suggestion is welcome!
>
> Thanks,
>
> --
> Weiwei Shi, Ph.D
> Research Scientist
> GeneGO, Inc.
>
> "Did you always know?"
> "No, I did not. But I believed..."
> ---Matrix III
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>


-- 
##################################################
Weibo Xie
National Center of Plant Gene Research (Wuhan).
National Key Laboratory of Crop Genetic Improvement
Huazhong Agricultural University Wuhan 430070, China
Phone: 86-27-61324632

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