RV: wgcna

0

Entering edit mode

Raquel Martinez Garcia ▴ 50

@raquel-martinez-garcia-4065

Last seen 10.3 years ago

=================================================== Raquel Mart?nez Garc?a Tlfn: (+34) 91 224 69 00 (ext 3015) e-mail: rmartinezg at cnio.es Unidad de Investigaci?n Cl?nica de Tumores Digestivos///Gastrointestinal Cancer Clinical Research Unit Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) =================================================== -----Mensaje original----- De: Martinez.Raquel Enviado el: mi? 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,verbo se=3,networkType="signed",nPermutations=2,maxGoldModuleSize=100,maxMod uleSize=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 : n?mero de items para para sustituir no es un m?ltiplo de la longitud del reemplazo =================================================== Raquel Mart?nez Garc?a Tlfn: (+34) 91 224 69 00 (ext 3015) e-mail: rmartinezg at cnio.es Unidad de Investigaci?n Cl?nica de Tumores Digestivos///Gastrointestinal Cancer Clinical Research Unit Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) =================================================== **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

Network Cancer Network Cancer • 1.7k views

ADD COMMENT • link updated 13.5 years ago by Robert Castelo ★ 3.4k • written 13.5 years ago by Raquel Martinez Garcia ▴ 50

0

Entering edit mode

Robert Castelo ★ 3.4k

@rcastelo

Last seen 2 days ago

Barcelona/Universitat Pompeu Fabra

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 Mart?nez Garc?a > Tlfn: (+34) 91 224 69 00 (ext 3015) > e-mail: rmartinezg at cnio.es > Unidad de Investigaci?n Cl?nica de Tumores Digestivos///Gastrointestinal Cancer Clinical Research Unit > Centro Nacional de Investigaciones Oncol?gicas > C.P.: 28029 Zip Code: 28029 > C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) > =================================================== > > > > > -----Mensaje original----- > De: Martinez.Raquel > Enviado el: mi? 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,ver bose=3,networkType="signed",nPermutations=2,maxGoldModuleSize=100,maxM oduleSize=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 : > n?mero de items para para sustituir no es un m?ltiplo de la longitud del reemplazo > > > =================================================== > Raquel Mart?nez Garc?a > Tlfn: (+34) 91 224 69 00 (ext 3015) > e-mail: rmartinezg at cnio.es > Unidad de Investigaci?n Cl?nica de Tumores Digestivos///Gastrointestinal Cancer Clinical Research Unit > Centro Nacional de Investigaciones Oncol?gicas > C.P.: 28029 Zip Code: 28029 > C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) > =================================================== > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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

ADD COMMENT • link 13.5 years ago Robert Castelo ★ 3.4k

0

Entering edit mode

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,maxModule Size=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) > > =================================================== > > > > > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los > ficheros adjuntos, pueden contener información protegida para el uso > exclusivo de su destinatario. Se prohíbe la distribución, reproducción o > cualquier otro tipo de transmisión por parte de otra persona que no sea el > destinatario. Si usted recibe por error este correo, se ruega comunicarlo al > remitente y borrar el mensaje recibido. > > **CONFIDENTIALITY NOTICE** This email communication and any attachments > may contain confidential and privileged information for the sole use of the > designated recipient named above. Distribution, reproduction or any other > use of this transmission by any party other than the intended recipient is > prohibited. If you are not the intended recipient please contact the sender > and delete all copies. > > > > > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los > ficheros adjuntos, pueden contener información protegida para el uso > exclusivo de su destinatario. Se prohíbe la distribución, reproducción o > cualquier otro tipo de transmisión por parte de otra persona que no sea el > destinatario. Si usted recibe por error este correo, se ruega comunicarlo al > remitente y borrar el mensaje recibido. > > **CONFIDENTIALITY NOTICE** This email communication and any attachments > may contain confidential and privileged information for the sole use of the > designated recipient named above. Distribution, reproduction or any other > use of this transmission by any party other than the intended recipient is > prohibited. If you are not the intended recipient please contact the sender > and delete all copies. > > > > > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los > ficheros adjuntos, pueden contener información protegida para el uso > exclusivo de su destinatario. Se prohíbe la distribución, reproducción o > cualquier otro tipo de transmisión por parte de otra persona que no sea el > destinatario. Si usted recibe por error este correo, se ruega comunicarlo al > remitente y borrar el mensaje recibido. > > **CONFIDENTIALITY NOTICE** This email communication and any attachments > may contain confidential and privileged information for the sole use of the > designated recipient named above. Distribution, reproduction or any other > use of this transmission by any party other than the intended recipient is > prohibited. If you are not the intended recipient please contact the sender > and delete all copies. > > > > _______________________________________________ > > 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 > > > > -- > 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 > > _______________________________________________ > 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 > -- 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=""> [[alternative HTML version deleted]]

ADD REPLY • link 13.5 years ago Tim Triche ★ 4.2k

Login before adding your answer.