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I get the seg-fault on exiting R after loading WGCNA into R-3.4.3 on
Linux. Valdgrind
shows the problem occurs when tearing down an Rstreambuf object:
% R --debugger valgrind --vanilla --quiet
==30889== Memcheck, a memory error detector
==30889== Copyright (C) 2002-2015, and GNU GPL'd, by Julian
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
Hi all,
I am using WGCNA for methylation level network construction e modules
detection.
In my network there are 26 modules with assigned colors and numeric labels,
id.
Which Is the best way to reassign different color to each module?
How to know the elements associated to each colored module in
Hi Giovanni,
please follow Tutorial I, section 3 (particularly 3d, "Summary output
of network analysis results") at
http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/index.html
. This will show you how to output module membership of each CpG into
a file. If you wa
Hi Pan,
On Wed, May 14, 2014 at 9:14 PM, Panos Bolan wrote:
> Dear list,
>
> Apologies for posting this to both Bioconductor and here. I recently read a
> Bioconductor post where the developer of the WGCNA suggested the use of the
> package for RNA-seq data analysis after implementing a variance
Dear list,
Apologies for posting this to both Bioconductor and here. I recently read a
Bioconductor post where the
developer of the WGCNA suggested the use of the package for RNA-seq data
analysis after implementing a variance stabilization normalization to
the raw counts. I have read the tuto
Hi Peter,
Thank you for your time and input on this matter. I will take your advice
and reconstruct the blocks using a different maximum cutoff and plot the
figures next to one another. I also wanted to thank you for creating the
WGCNA package and including the section on exporting to other visual
Hi Derek,
the simple answer is that the block-specific dendrograms cannot be
meaningfully combined into a single dendrogram. You have to plot them
separately. You can create a multi-panel figure that shows all block
dendrograms in one big figure, although with 10 blocks I would not
necessarily att
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
On Wed, Aug 1, 2012 at 6:30 AM, Ingezz wrote:
> Dear Peter,
>
> I have another question about WGCNA. I am using the package for
> meta-analysis to find modules preserved in several datasets. However, I am
> unsure how to handle the softpower, because each dataset has its own ideal
> scale indepenc
Dear Peter,
I have another question about WGCNA. I am using the package for
meta-analysis to find modules preserved in several datasets. However, I am
unsure how to handle the softpower, because each dataset has its own ideal
scale indepence value. When combining several datasets what should I do?
Peter,
Thank you. In fact, I am also very interesting to WGCNA.
On Sat, Jun 16, 2012 at 3:29 AM, Peter Langfelder
wrote:
> On Fri, Jun 15, 2012 at 8:04 AM, Ingezz wrote:
>> Dear Peter,
>>
>> I am trying to apply the WGCNA meta-analysis for two (or more) microarray
>> datasets-tutorial to my own
On Fri, Jun 15, 2012 at 8:04 AM, Ingezz wrote:
> Dear Peter,
>
> I am trying to apply the WGCNA meta-analysis for two (or more) microarray
> datasets-tutorial to my own data.
>
>> mp=modulePreservation(multiExpr,multiColor,referenceNetworks=1,verbose=3,networkType="signed",
>> nPermutations=30,max
Dear Peter,
I am trying to apply the WGCNA meta-analysis for two (or more) microarray
datasets-tutorial to my own data.
> mp=modulePreservation(multiExpr,multiColor,referenceNetworks=1,verbose=3,networkType="signed",
>
> nPermutations=30,maxGoldModuleSize=100,maxModuleSize=400)
However, the e
Hi Meeta,
yes, there was a bug in the package. Please install the newest version
and try again.
Best,
Peter
On Tue, Jul 12, 2011 at 1:20 PM, mistrm wrote:
> Hi Peter and Raquel
>
> I am following the same tutorial and seem to have the same error appear and
> I am using 30 permutations (code be
Hi Peter and Raquel
I am following the same tutorial and seem to have the same error appear and
I am using 30 permutations (code below). Is it a bug or something that I can
easily fix? I'm not quite sure how to interpret the error.
multiExpr = list(A1=list(data=t(ctl)),A2=list(data=t(sz)))
multiC
On Wed, Jul 6, 2011 at 8:27 AM, Raquel Martinez Garcia
wrote:
> 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
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
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