R help - Jul 2011 - wgcna

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(multiExpr,multiColor,referenceNetworks=1,verbose=3,networkType="signed",nPermutations=2,maxGoldModuleSize=100,maxModuleSize=400)
   ..checking data for excessive amounts of missing data..
      Flagging genes and samples with too many missing values...
       ..step 1
      Flagging genes and samples with too many missing values...
       ..step 1
   ..unassigned 'module' name: grey
   ..all network sample 'module' name: gold
   ..calculating observed preservation values
   ..calculating permutation Z scores
  ..Working with set 1 as reference set
  ....working with set 2 as test set
   ......working on permutation 1
   ......working on permutation 2
Error en zAll[, stat] = z :
   número de items para para sustituir no es un múltiplo de la longitud del
reemplazo
   (number of items  to replace  is not a  multiple of&nbs
p;replacement  length)

-- 
********************************************

Raquel Martinez Garcia, Graduate Student
Gastrointestinal Cancer Clinical Research Unit
&  Structural Biology and BioComputing Programme
Spanish National Cancer Research Center (CNIO)
Melchor Fernandez Almagro, 3.
28029 Madrid, Spain.
Phone: +34 91 732 80 00 #3015
rmartinezg@cnio.es
http://www.cnio.es

********************************************



**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y ...{{dropped:7}}

On Wed, Jul 6, 2011 at 8:27 AM, Raquel Martinez Garcia
<rmartinezg at cnio.es> 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 you know, what is happens?
Hi Raquel,

I'm the author of the function. I see you have already modified the
tutorial with your own input. The error you see may be a bug in the
function, but it may also be due to the fact that you use only 2
permutations. I suggest you try to increase the number of permutations
to at least 10, but for meaningful results you should use at least 50.

HTH,

Peter

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? 
- pick the lowest scale indepence value and use this for all datasets? 
- calculate an average scale indepence value of the datasets, and use this
one? 
- use different scale indepence values for different datasets, all though
combining them later on? 
- or something else, which I havent thought of? 

Hope you can help me! 

Many thanks! 

Kind regards,
Inge



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