Dear Pankaj

none (packaged) that I would be aware of, as you don't even have an AM 
matrix (this should be square by definition.

Now the best would probably be to write yourself something to convert 
your special matrix into an edge list. Or if you feel lazy just bring 
the matrix up to full size by padding with zeroes (as you seem to be 
only interested in metabolite transcript correlations)

Cheers,
Björn
> Dear Prof. Björn Usadel,
>
>
> I could generate the Adjacency out of the gene metabolite correlation.
>
>   
>> m<-matrix(rnorm(1000),nrow=100,ncol=10,dimnames=list(paste("met",c(1:100))))
>> g<-matrix(rnorm(10000),nrow=1000,ncol=10,dimnames=list(paste("gen",c(1:1000))))
>> cm<-cm <- cor(t(m),t(g))
>> cm<-cor(t(m),t(g))
>> ADJ<-ifelse(c(cm)>0.75,1,0)
>> dim(ADJ)<-dim(cm)
>> str(ADJ)
>>     
>  num [1:100, 1:1000] 0 0 0 0 0 0 0 0 0 0 ...
>
> Now need to convert the ADJ to a edge list or sif. I have tried igraph package. But, it can convert square Adjacency matrix to edge list or a graphNEL object. Is there a way that I can convert my non square AM to a graph object or edge list ?
>
> Thanks,
>  
> Pankaj 
>
>
> ________________________________
>  From: Sean Davis <sdavis2@mail.nih.gov>
> To: B Usadel <b.usadel@bio1.rwth-aachen.de> 
> Cc: pankaj borah <pankajborah2k3@yahoo.co.in>; "bioconductor@r-project.org" <bioconductor@r-project.org> 
> Sent: Saturday, 3 March 2012 1:23 PM
> Subject: Re: [BioC] Gene-Metabolite correlation network
>  
> On Fri, Mar 2, 2012 at 9:35 AM, B Usadel <b.usadel@bio1.rwth-aachen.de> wrote:
>   
>> This would be a crude solution but will do the job
>> m<-matrix(rnorm(1000),nrow=100,ncol=10,dimnames=list(paste("met",c(1:100))))
>> g<-matrix(rnorm(10000),nrow=1000,ncol=10,dimnames=list(paste("gen",c(1:1000))))
>>     
>
> cm <- cor(t(m),t(g))
>
> No need for the rbind, I don't think.
>
> Sean
>
>
>   
>> mg<-rbind(m,g)
>> cm<-cor(t(mg))
>>
>> res<-cm[1:100,101:1100]
>>
>> For networks, you can try the GeneNet package using the mixed matrix. Or
>> just use res above with some sensible threshold and then make an
>> adjacency matrix out of it and convert it into a graphNEL object.
>>
>> (This is all assuming Pearson correlation (or derivatives thereof) is
>> the way to go between metabolites and transcripts)
>>
>> Cheers,
>> -björn
>>
>>     
>>> Thank you Prof. Björn,
>>>
>>> Yes they are are  10 identical conditions. But two matrices  are of
>>> not the same dimension. A has 1000 genes (rows) and B has 100
>>> metabolites(rows).
>>>
>>> Is there any package available in Bio-conductor or R  for generating
>>> gene -metabolite correlation network ?
>>>
>>> Regards,
>>>
>>> Pankaj2k3
>>>
>>>       
>
>   
>>> ------------------------------------------------------------------------
>>> *From:* B Usadel <b.usadel@bio1.rwth-aachen.de>
>>> *To:* pankaj borah <pankajborah2k3@yahoo.co.in>
>>> *Cc:* "bioconductor@r-project.org" <bioconductor@r-project.org>
>>> *Sent:* Friday, 2 March 2012 4:13 PM
>>> *Subject:* Re: [BioC] Gene-Metabolite correlation network
>>>
>>> Hi Pankaj
>>>
>>> if it is the same 10 conditions, I would merge the matrices.
>>> (Otherwise subset both matrices on the identical conditions)
>>> And then calculate the whole correlation/covariance matrix and extract
>>> the relevant regions, With this small number of genes, it will be done
>>> almost instantaneously.
>>>
>>> Cheers,
>>> björn
>>>       
>>>> Hi All,
>>>>
>>>> I have two matrices   A and B.
>>>> A contains expression values for 1000 genes in 10 conditions  A[1:1000,1:10]
>>>> B contains metabolic profiles of 100 metabolites in 10 conditions B[1:100,1:10]
>>>>
>>>> Is there a way that I can calculate gene-metabolite correlation OR co-variance  matrix using A and B ?
>>>>
>>>> Thanks
>>>>
>>>> Pankaj2k3
>>>>      [[alternative HTML version deleted]]
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor@r-project.org <mailto:Bioconductor@r-project.org>
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>         
>>> --
>>> Make the (Gabi) primary database better by just taking a short questionaire:
>>> https://www.surveymonkey.com/s/RK3GMPC
>>>
>>> Prof. Dr. Björn Usadel
>>> RWTH Aachen University
>>> Institute for Biology I
>>> Worringer Weg 1
>>> 52056 Aachen
>>>
>>> phone: +49 (0)241 80 26634
>>> fax:   +49 (0)241 80 22637
>>> web:   http://www.usadellab.org
>>> ---
>>>
>>>
>>>
>>>       
>> --
>> Make the (Gabi) primary database better by just taking a short questionaire:
>> https://www.surveymonkey.com/s/RK3GMPC
>>
>> Prof. Dr. Björn Usadel
>> RWTH Aachen University
>> Institute for Biology I
>> Worringer Weg 1
>> 52056 Aachen
>>
>> Forschungszentrum Jülich
>> IBG-2: Plant Sciences
>> 52425 Jülich
>> Germany
>>
>> phone: +49 (0)241 80 26634
>> fax:   +49 (0)241 80 22637
>> web:   http://www.usadellab.org
>> ---
>>
>>
>>        [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>     


-- 
Make the (Gabi) primary database better by just taking a short questionaire:
https://www.surveymonkey.com/s/RK3GMPC

Prof. Dr. Björn Usadel
RWTH Aachen University
Institute for Biology I
Worringer Weg 1
52056 Aachen

Forschungszentrum Jülich
IBG-2: Plant Sciences
52425 Jülich
Germany

phone: +49 (0)241 80 26634
fax:   +49 (0)241 80 22637
web:   http://www.usadellab.org
---


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