Search
Question: WGCNA RNAseq
0
gravatar for Anna Esteve Codina
3.7 years ago by
Anna Esteve Codina20 wrote:
Dear Peter, I successfully run the WGCNA software with RNAseq data after TMM normalization and log-transformation. But I have some questions: 1.- Is it necessary to clean the input dataset of genes before running the analysis? I have around 20,000 expressed genes, whereas in the Tutorial there are only ~3000 genes. Should I take only the most variable ones? 2.- I correlated the modules with two continuous traits but I did not obtain any significant at the module level, but I did at the gene level. Is it possible to have significant genes associated with a trait and other not significant within the same module? 3.- I have modules with up to 4000 genes, how can it be? Thanks for the explanations, Anna Esteve Codina, PhD Functional Bioinformatics Team Centre Nacional d?An?lisi Gen?mica (Parc Cient?fic de Barcelona) Baldiri Reixac 4-6, Torre I www.cnag.cat aesteve at pcb.ub.cat -----Mensaje original----- De: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] En nombre de Peter Langfelder Enviado el: lunes, 17 de febrero de 2014 4:02 Para: Martin Morgan CC: bioconductor at r-project.org Asunto: Re: [BioC] WGCNA Hi Martin, if you simply run pickSoftThreshold without calling enableWGCNAThreads before, the function is run in a single-worker mode. To reproduce the error, you have to call enableWGCNAThreads with an argument of 2 or more. For a reproducible example, you can run the first two sections of WGCNA Tutorial I at http://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/Rpack ages/W GCNA/Tutorials/index.html. Sorry, I don't have a quick simulated example ready but could cook one up. I am actually not sure whether this problem also occurs on Windows, since the cluster parallelization is very different from the forking on linux. I am only aware of it through bug reports of WGCNA users (who usually email me directly). Peter On Sun, Feb 16, 2014 at 6:30 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > > but from my original mail pickSoftThreshold 'worked for me' under > Rstudio on Windows (output below, again); maybe I didn't invoke it in > a way that would trigger the error, so a reproducible illustration > would help (me). Also on Windows (platform of the original post) the > parallel package doesn't fork, e.g., from ?mcfork > > These are low-level functions, not available on Windows, and not > exported from the namespace. > > or ?mclapply > > It relies on forking and hence is not available on Windows unless > 'mc.cores = 1'. > > Do you mean something less literally forking, like spawning a new process? > Maybe from > > http://stackoverflow.com/questions/20704235 > > the solution is as simple as adding .packages="WGCNA" to your foreach calls? > > >> x = pickSoftThreshold(data) > trace: .C("checkAvailableMemoryForR", size = as.double(size), PACKAGE > = > "WGCNA") > trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), > ncolx = as.integer(ncol(x)), > y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick), > cosineX = as.integer(cosineX), cosineY = as.integer(cosineY), > res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err), > nThreads = as.integer(nThreads), verbose = as.integer(verbose), > indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE = > "WGCNA") > trace: .C("corFast", x = as.double(x), nrow = as.integer(nrow(x)), > ncolx = as.integer(ncol(x)), > y = as.double(y), ncoly = as.integer(ncol(y)), quick = as.double(quick), > cosineX = as.integer(cosineX), cosineY = as.integer(cosineY), > res = as.double(bi), nNA = as.integer(nNA), err = as.integer(err), > nThreads = as.integer(nThreads), verbose = as.integer(verbose), > indent = as.integer(indent), DUP = FALSE, NAOK = TRUE, PACKAGE = > "WGCNA") > Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k. > 1 1 0.173 -11.00 0.98400 4.02e+01 4.02e+01 4.45e+01 > 2 2 0.326 -8.45 0.95700 5.04e+00 5.04e+00 6.12e+00 > 3 3 0.241 -4.30 0.95300 8.01e-01 8.02e-01 1.05e+00 > 4 4 0.348 -4.04 0.95000 1.49e-01 1.49e-01 2.25e-01 > 5 5 0.513 -3.74 0.90400 3.15e-02 3.09e-02 5.77e-02 > 6 6 0.697 -3.72 0.92600 7.32e-03 6.99e-03 1.70e-02 > 7 7 0.811 -3.26 0.93300 1.85e-03 1.70e-03 5.55e-03 > 8 8 0.893 -2.92 0.95700 4.99e-04 4.32e-04 1.97e-03 > 9 9 0.923 -2.67 0.94400 1.43e-04 1.15e-04 7.35e-04 > 10 10 0.958 -2.38 0.96500 4.34e-05 3.15e-05 2.85e-04 > 11 12 0.910 -2.07 0.88600 4.50e-06 2.59e-06 4.55e-05 > 12 14 0.325 -3.02 0.21800 5.31e-07 2.29e-07 7.58e-06 > 13 16 0.219 -3.01 0.00942 6.88e-08 2.06e-08 1.29e-06 > 14 18 0.206 -3.06 0.03550 9.53e-09 1.93e-09 2.29e-07 > 15 20 0.227 -2.97 0.02620 1.39e-09 1.85e-10 4.11e-08 > > > > >> >> Hope this clears up any lingering confusion. >> >> Also see inline below >> >> On Sun, Feb 16, 2014 at 12:26 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> >> wrote: >> >>> >>> >>> Also I don't see where the error message is coming from (who is >>> printing "task 1 failed - " ?) >> >> >> >> I believe this is printed by foreach/doParallel but here I could be wrong. >> >> >> >> HTH, >> >> Peter >> >>> >>> I have a vague recollection that the x[["Version"]] (which comes >>> from >>> getAnywhere("print.sessionInfo")) has to do with multiple installed >>> versions of a package, but again it would be good to get to the >>> bottom of this problem. >>> >>> Martin > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 _______________________________________________ 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 ---------------------------------------------------------------------- ------ ----------------------- Texto aqadido por Panda Security for Desktops: Este mensaje NO ha sido clasificado como SPAM. Si se trata de un mensaje de correo no solicitado (SPAM), haz clic en el siguiente vmnculo para reclasificarlo: http://localhost:6083/Panda?ID=pav_7520&SPAM=true&path=C:\Windows\syst em32\c onfig\systemprofile\AppData\Local\Panda%20Software\AntiSpam ---------------------------------------------------------------------- ------
ADD COMMENTlink written 3.7 years ago by Anna Esteve Codina20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 308 users visited in the last hour