There's also the nicely documented 'linkcomm' package (again on CRAN) which
was recently published in Bioinformatics.  To my mind, it provides a more
straightforward means of doing some tasks usually associated with the WGCNA
package.

However, please note that Steve Horvath and his colleagues have been quite
responsive in the past when people reported problems or suggestions for
WCGNA.  The original poster might find it useful to try contacting them (the
authors) directly.


On Wed, Jul 6, 2011 at 9:29 AM, Robert Castelo <robert.castelo@upf.edu>wrote:

> Dear Raquel,
>
> as far as i can tell from the BioC website, WGCNA is not a Bioconductor
> package and therefore you're more likely to get support for the problem
> below if you contact the authors of the package directly.
>
> a shameless advertisement from my side :) just in case you have not look
> at it, and depending on what you are interested to do, the BioC package
> qpgraph, for which you can get support in this list, aims also at
> inferring molecular regulatory networks from microarray expression data.
> Its url at the BioC website is:
>
> http://www.bioconductor.org/packages/release/bioc/html/qpgraph.html
>
> best regards,
>
> robert.
>
> On Wed, 2011-07-06 at 16:48 +0200, Martinez.Raquel wrote:
> >
> > ===================================================
> > Raquel Martínez García
> > Tlfn: (+34) 91 224 69 00 (ext 3015)
> > e-mail: rmartinezg@cnio.es
> > Unidad de Investigación Clínica de Tumores Digestivos///Gastrointestinal
> Cancer Clinical Research Unit
> > Centro Nacional de Investigaciones Oncológicas
> > C.P.: 28029                Zip Code: 28029
> > C/. Melchor Fernández Almagro, 3    Madrid (Spain)
> > ===================================================
> >
> >
> >
> >
> > -----Mensaje original-----
> > De: Martinez.Raquel
> > Enviado el: mié 06/07/2011 16:47
> > Para: bioconductor@staz.math.ethz.ch
> > Asunto: wgcna
> >
> > Hi,
> >
> > I have an error with modulePreservation (WGCNA package). Does anyone know
> what happens??
> > The error is below.
> >
> >
> > Thanks
> > Raquel
> >
> >
> > multiExpr = list(A = list(data=t(badea)),B = list(data=t(mayo)))
> > # two independent datasets. dim = 13447 x 36)
> > mp =
> modulePreservation(multiExpr,multiColor,referenceNetworks=1,verbose=3,networkType="signed",nPermutations=2,maxGoldModuleSize=100,maxModuleSize=400)
> >   ..checking data for excessive amounts of missing data..
> >      Flagging genes and samples with too many missing values...
> >       ..step 1
> >      Flagging genes and samples with too many missing values...
> >       ..step 1
> >   ..unassigned 'module' name: grey
> >   ..all network sample 'module' name: gold
> >   ..calculating observed preservation values
> >   ..calculating permutation Z scores
> >  ..Working with set 1 as reference set
> >  ....working with set 2 as test set
> >   ......working on permutation 1
> >   ......working on permutation 2
> > Error en zAll[, stat] = z :
> >   número de items para para sustituir no es un múltiplo de la longitud
> del reemplazo
> >
> >
> > ===================================================
> > Raquel Martínez García
> > Tlfn: (+34) 91 224 69 00 (ext 3015)
> > e-mail: rmartinezg@cnio.es
> > Unidad de Investigación Clínica de Tumores Digestivos///Gastrointestinal
> Cancer Clinical Research Unit
> > Centro Nacional de Investigaciones Oncológicas
> > C.P.: 28029                Zip Code: 28029
> > C/. Melchor Fernández Almagro, 3    Madrid (Spain)
> > ===================================================
> >
> >
> >
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> > _______________________________________________
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>
> --
> Robert Castelo, PhD
> RyC Fellow Researcher
> Dept. Experimental and Health Sciences
> Pompeu Fabra University
> Barcelona Biomedical Research Park
> Dr. Aiguader 88
> E-08025 Barcelona, Spain
> tel +34 933 160 514
> fax +34 933 160 550
> robert.castelo@upf.edu
>
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-- 
If people do not believe that mathematics is simple, it is only because they
do not realize how complicated life is.
John von Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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