Re: [R] [BioC] similarity between two gene lists with varied length

From: Weiwei Shi <helprhelp_at_gmail.com>
Date: Sun, 24 Aug 2008 09:30:59 +0800

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_at_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_at_stat.math.ethz.ch [
> bioconductor-bounces_at_stat.math.ethz.ch] On Behalf Of Weiwei Shi [
> helprhelp_at_gmail.com]
> Sent: Saturday, August 23, 2008 7:55 PM
> To: r-help_at_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
>
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>
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-- 
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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