fairmiracle/moda

MOdule Differential Analysis for weighted gene co-expression network

moda's Issues

could not find function "WeightedModulePartitionAmoutain"

Is there any explanation on why many functions, which are described in the manual, are not available?

Issue with ModuleFrequency function

Hi,
I am interested in your MODA package. I used the synthetic data you provided with the package, splitting datExpr1 into two dataset with 10 replicates each (hypothetically belonging to two different treatments) and using datExpr2 as the dataset with all the conditions together.
I determined the modules for each condition (the two dataset originated from splitting datExpr1 and the dataset from datExpr2) with "WeightedModulePartitionHierarchical". Then I managed to compare all the network using "CompareAllNets" function which identified the specific modules for each condition.
I want now to determine the frequency of condition specific modules using the function "ModuleFrequency" but I get the following error messages:

Error in uniqueaffiliation[[tmp[j]]] <- union(uniqueaffiliation[[tmp[j]]], : attempt to select more than one element in integerOneIndex In addition: Warning message: In brewer.pal(Ncon, "Set1") : minimal value for n is 3, returning requested palette with 3 different levels

I was wondering if you can help me with this? Maybe I am not following the correct procedure or I am missing some steps? could you help me on this?
Thanks a lot
Luca

Information about MODA

I would like to read more about the package, I found the preprint, but is there a published article of the package?

As a technical notes on the package:
When loading the package I get two warnings, see the vignette for instance.
In WeightedModulePartitionAmoutain and in WeightedModulePartitionLouvain there are print functions instead of a message to the user which confused me initially.

Many thanks