similar to: wgcna

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 again. Peter On Sun, Jul 9, 2017 at 2:29 AM, Ankush Sharma <ankush.sak at

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

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

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'm attaching two

Hi all, Hope someone could help me. I am trying to run automatically the conversion of an Rwn file to a tex file. I am using windows 7, and cygwin. I tried to run automatically the Sweave.sh script, in its the most recent version available at R webpage: http://cran.r-project.org/contrib/extra/scripts/Sweave.sh Unfortunately, I got this error message: =========================== Raquel at

Hi all, I would like to compute ergodic mean using MCMC output from WinBUGS. I tried using CODA package, but it seems that it is not implemented yet. Could anyone help me to compute this? Attached to this email are my output and index files. Kind regards, Raquel -- Raquel Rangel de Meireles Guimar?es Doutoranda em Demografia raquel at cedeplar.ufmg.br

Hi all, I have two basic questions, hope you should help me: 1. How do I save a log file in R with the results? For example, in Stata it can be done by using "log using c:\...\test.txt" 2. How do I display the execution time of one function like the one below: CalculaCorrelacao <- function(construto, n) { library(polycor) for (i in 2:n){ for (j in i:n+1){ x1

Is there any implicit function in R to minimize a function with many variables? Many thanks Raquel ---------------------- R Granell, Rheumatology Unit & School of Mathematics University of Bristol Raquel.Granell at bristol.ac.uk Tel:07968079410

Hi all, I'm trying to set up the Windows Rtools toolset for building packages with compiled code. I installed for Windows R-3.4.3 from CRAN and installed 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).

This may sound crazy but... I have data like this... > results.matrix [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [1,] 949 93 2 11 26 20 7 6 10 5 0 3 [2,] 1233 124 24 35 58 57 17 21 31 19 11 21 Which is the result of binning (summing) the response variables of an underlying (nearly) continious range of predictor

I''ve run across something that would save me days of trouble. Situation, the contents of one ZFS file system needs to be moved to another ZFS file system. The destination can be the same Zpool, even a brand new ZFS file system. A command to move the data from one ZFS file system to another, WITHOUT COPYING, would be nice. At present, the data is almost 1TB. Ideally a "zmv" or

I can confirm the behaviour that you report.? Usually I put Rtools in c:\programs\Rtools and modify the path accordingly. Recently (don't recall for how long) I have encountered the same problems as you have and I have resorted to moving Rtools to c:\Rtools I have no idea as how to proceed; perhaps it could be worth trying an older version of Rtools (though that may cause other problems).

Hello, I want to use optim with simulated data. My program generates a sample and then calls optim to optimise a function that depends on the generated sample. I want to do this with 100 samples. But optim does not 'work' for the 100 samples, sometimes I get a message saying that sigma matrix was not invertible and therefore the optimisation was not carried out, and then my program

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello: My name is Ruben and I am from Elche (Spain) We are trying to setup a Samba server in our network. Our server is Suse Linux 7.3 Professional, with this version of samba: at:/ # smbd -V Version 2.2.1a at:/ # nmbd -V Version 2.2.1a I think that smbd is running OK becouse we can access to the server using its IP from the outside. But Server

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

Hello, a user of one of my packages has sent me the following problem that apparently appears when loading the tcltk package. I'm guessing something (Tcl/Tk? R open scripting framework?) is not installed correctly... can someone please confirm or correct my guess? The OS is Mac 10.6.5. Thanks, Peter This is what I get: > ~ joseoter$ r > R version 2.12.0 (2010-10-15) > Copyright

Hello, <http://tolstoy.newcastle.edu.au/R/help/04/07/0312.html#0313qlink1> Could anybody tell me how to generate discrete Laplacian distribution? I need to sample uma discretised Laplacian density like this: J( g -> g´) ~ exp (-lambda | g´ - g |) g in {0,…, gmax} Thanks, Nicolette [[alternative HTML version deleted]]

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 the matching name - does the speed of this depend on how functions are

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

It seems like many of the multi-threaded BLASes have some sort of fundamental problem preventing use in the way Juan suggests: - Dirk's vignette states that ATLAS "fixes the number of cores used at compile-time and cannot vary this setting at run-time", so any user-friendly implementation for R would have to compile ATLAS for 1-16 threads to allow the user to switch at run-time.