[BioC] RV: wgcna

[Robert Castelo]

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 at 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 at 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 at 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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-- 
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 at upf.edu