search for: wgcna

Hi all, a user contacted me about a segfault when installing WGCNA package dowloaded from CRAN. I also see a segfault like that on certain installs of R. The package passes all CRAN checks, so presumably this has something to do with the R installation or environment. The R versions here are not the newest but I would guess that this is not an R version issue. I...

...talled Rtools-3.4 in a custom location M:\R\R-3.4.3 and M:\R\Rtools-3.4 Following the instructions, in shell, I set Path=M:\R\Rtools-3.4\bin;M:\R\Rtools-3.4\gcc-4.6.3\bin;M:\R\R-3.4.3\bin;... (the ... are other paths irrelevant for R/Rtools). When I run M:\Work\RLibs>R.exe CMD INSTALL --build WGCNA I get the following ouput: In R CMD INSTALL * installing to library 'M:/R/R-3.4.3/library' * installing *source* package 'WGCNA' ... ** libs *** arch - i386 c:/Rtools/mingw_32/bin/g++ -I"M:/R/R-3.4.3/include" -DNDEBUG -O2 -Wall -mtune=generic -c bucketApproxSort.cc -o...

Hi, I'm running a tutorial ("Meta-analyses of data from two (or more) microarray data sets"), which use wgcna package. I have an error in the function modulePreservation (it is below). I'm using R2.13 Can you help me? Do you know, what is happens? Thanks Raquel multiExpr = list(A = list(data=t(badea)),B = list(data=t(mayo))) # two independent datasets (dim = 13447 x 36) mp = modulePreservation(mult...

Hello fellow R users, I am currently learning to use R, so please forgive me if there is an obvious explanation for the following problem. My goal is to perform WGCNA on a dataset of 19776 genes, so I opted to follow the block-wise network construction (Section 2c) in the WGCNA R Tutorial by Peter Langfelder and Steve Horvath. I ended up with 10 blocks and am able to plot the dendrograms and module colors for each block, but I am having trouble grouping all of...

First, please read WGCNA FAQ at https://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/faq.html regarding using RNA-seq and other count data. Second, if you insist on using WGCNA on raw count data (which I don't recommend), use something like storage.mode(datExpr) = "double" and try aga...

Dear all , I would like to reconstruct coexpression networks from proteomic count data having integer values. Some internal function doesn't like to work well with integers. How can this error be rectified? > adjacency = adjacency(datExpr, power = softPower, type = "signed"); Error in cor(datExpr, use = "p") : REAL() can only be applied to a 'numeric', not a

...and > M:\R\Rtools-3.4 > > Following the instructions, in shell, I set > Path=M:\R\Rtools-3.4\bin;M:\R\Rtools-3.4\gcc-4.6.3\bin;M:\R\R- > 3.4.3\bin;... > (the ... are other paths irrelevant for R/Rtools). > > When I run > > M:\Work\RLibs>R.exe CMD INSTALL --build WGCNA > > I get the following ouput: > > In R CMD INSTALL > * installing to library 'M:/R/R-3.4.3/library' > * installing *source* package 'WGCNA' ... > ** libs > > *** arch - i386 > c:/Rtools/mingw_32/bin/g++??-I"M:/R/R-3.4.3/include" -DNDEBUG &...

Hi, I am have a data set of around 43000 probes(rows), and have to calculate correlation matrix. When I run cor function in R, its throwing an error message of RAM shortage which was obvious for such huge number of rows. I am not getting a logical way to cut off this huge number of entities, is there an alternative to pearson correlation or with other dist() methods calculation(euclidean) that

...to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > [Previously saved workspace restored] > > > library(WGCNA) > Loading required package: impute > Loading required package: dynamicTreeCut > Loading required package: flashClust > > Attaching package: 'flashClust' > > The following object(s) are masked from 'package:stats': > > hclust > > Loading required...

Hi all, I maintain the WGCNA package which at present has nearly 200 functions. In the future there will be more. Curious whether it would be preferable or useful to split the package into a couple different ones with different aims. Obviously, when one calls a function in R, package name spaces have to be traversed to find th...

Dear All, I am using the plotrix library to plot some matrices. I have a problem: some of my data are outliers, hence using a linear color scale does not work very well (you would see too many cells having a similar, indistinguishable color). See the code snipped at the end of the email. Plotting the logarithm of the data gets the job done, but my problem is that I would like to write in every

...hes. Has anyone tried ExBLAS for use with R? On Sun, Dec 17, 2017 at 1:03 PM, Peter Langfelder < peter.langfelder at gmail.com> wrote: > I would be very cautious about OpenBLAS in particular... from time to > time I get complains from users that compiled code calculations in my > WGCNA package crash or produce wrong answers with large data, and they > all come from OpenBLAS users. I am yet to reproduce any of their > crashes when using MKL and ATLAS BLAS implementations. > > Just my 2 cents... > > Peter > > On Sat, Dec 16, 2017 at 12:28 PM, Kenny Bell <...

Dear R-Help, I have a clustering problem with hclust that I hope someone can help me with. Consider the classic hclust example: hc <- hclust(dist(USArrests), "ave") plot(hc) I would like to cut the tree up in such a way so as to avoid small clusters, so that we get a minimum number of items in each cluster, and therefore avoid singletons. e.g. in this example, you can see

Hi All, is there any effiective and dense/compact method to calculate the mean of a list of - of course coincident - matrices on an element by element basis? The resulting matrix' [i, j]-th element is the mean of the list's matrices' [i, j]-th elements respectively... Iterating by for statement is quite straightforward, but I am seeking for a more elegant solution, and my attempt with

Dear all, I've been trying to find how to compare tow different heatmaps but I'm having trouble getting the colors bar to be the same. I'm doing something like the following: library(gplots) dat<-cor(matrix(rnorm(100, m=10), nrow=10)) mat<-cor(matrix(rnorm(100), nrow=10)) dev.new() heatmap.2(mat, Rowv=NA, Colv=NA, col=redgreen(75), symm=TRUE, trace="none",

I am in need of someone's help in correlating gene expression. I'm somewhat new to R, and can't seem to find anyone local to help me with what I think is a simple problem. I need to obtain pearson and spearman correlation coefficients, and corresponding p-values for all of the genes in my dataset that correlate to one specific gene of interest. I'm working with mouse Affymetrix

...On Sun, Dec 17, 2017 at 1:03 PM, Peter Langfelder < > > peter.langfelder at gmail.com> wrote: > > > >> I would be very cautious about OpenBLAS in particular... from time to > >> time I get complains from users that compiled code calculations in my > >> WGCNA package crash or produce wrong answers with large data, and they > >> all come from OpenBLAS users. I am yet to reproduce any of their > >> crashes when using MKL and ATLAS BLAS implementations. > >> > >> Just my 2 cents... > >> > >> Peter >...

...der at gmail.com > <https://stat.ethz.ch/mailman/listinfo/r-devel>> wrote: />>/> />>/>> I would be very cautious about OpenBLAS in particular... from time to />>/>> time I get complains from users that compiled code calculations in my />>/>> WGCNA package crash or produce wrong answers with large data, and > they />>/>> all come from OpenBLAS users. I am yet to reproduce any of their />>/>> crashes when using MKL and ATLAS BLAS implementations. />>/>> />>/>> Just my 2 cents... />>/&gt...

Hello, I have a self-defined function to be computed on each column in a matrix. The basic idea is to ignore the elements that have value of 0 during computation. I should be able to write my own function but it could be computational expensive, so I'd love to ask if anyone may have suggestions on how to implement it more efficiently. Thanks in advance. For example, there are three

...information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. However, as soon as I try to use limma (or WGCNA... I haven't tried other packages yet) the following mistake pops up ( lapack routines cannot be loaded ) >library(limma) > fit <- lmFit(Data.rma, design) Error in chol2inv(fit$qr$qr, size = fit$qr$rank) : lapack routines cannot be loaded In addition: Warning message: In chol2inv(...