Question: Package "geNetClassifier": is this an "igraph' error?
0
gravatar for alakatos
4.1 years ago by
alakatos100
United States
alakatos100 wrote:

Hello All,

I tried to run the tutorial of "geNetClassifier" but an error stopped the process. I do believe I followed the tutorial line by line.

 I was wondering if this is an "igraph" bug or  I was doing something I am not aware of.

Thank you for your help.

Best,

Anita

Code:

library("leukemiasEset")
data("leukemiasEset")
summary(leukemiasEset$LeukemiaType)
ALL AML CLL CML NoL 
 12  12  12  12  12 
data(geneSymbols)
trainSamples <- c(1:10, 13:22, 25:34, 37:46, 49:58)
summary(leukemiasEset$LeukemiaType[trainSamples])
ALL AML CLL CML NoL 
 10  10  10  10  10 
leukemiasClassifier <- geNetClassifier(eset=leukemiasEset[,trainSamples],sampleLabels="LeukemiaType", plotsName="leukemiasClassifier",skipInteractions=TRUE, maxGenesTrain=20, geneLabels=geneSymbols)
10:23:53 - Filtering data and calculating the genes ranking...
10:24:28 - Calculating correlations between genes...
Network calculated without interactions
Gene associations (network) calculated between genes with posterior probability over 0.95
10:24:28 - All required parameters have been calculated and checked. Building classifier...
10:24:45 - Classifier trained with 50 samples.
Total number of genes included in the classifier: 32
Number of genes per class: 
 	ALL: 8 genes
 	AML: 5 genes
 	CLL: 4 genes
 	CML: 3 genes
 	NoL: 12 genes
No associations/redundancy was removed between these genes

Attaching package: ‘igraph’

The following objects are masked from ‘package:BiocGenerics’:

    normalize, union

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Error in layout_with_fr(list(100, FALSE, c(1, 2, 2, 3, 3, 3, 4, 4, 4,  : 
  unused argument (niterNumeric = 500)
sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
   
attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] igraph_1.0.1          RColorBrewer_1.1-2    cluster_2.0.3        
 [4] leukemiasEset_1.4.0   geNetClassifier_1.8.0 minet_3.26.0         
 [7] EBarrays_2.32.0       lattice_0.20-33       Biobase_2.28.0       
[10] BiocGenerics_0.14.0  

loaded via a namespace (and not attached):
[1] magrittr_1.5 class_7.3-12 tools_3.2.1  grid_3.2.1   e1071_1.6-6 
 

>

 
ADD COMMENTlink modified 4.1 years ago by saibar20 • written 4.1 years ago by alakatos100

Yes, igraph made extensive changes and this caused many packages that depend on it (including geNetClassifier) to break.

The maintainer of geNetClassifier has been notified about this issue so I would hope that it would be resolved soon. I will also notify them about this thread.

ADD REPLYlink written 4.1 years ago by Dan Tenenbaum8.2k

Thank you.

Anita

ADD REPLYlink written 4.1 years ago by alakatos100
Answer: Package "geNetClassifier": is this an "igraph' error?
0
gravatar for saibar
4.1 years ago by
saibar20
University of Salamanca, Spain / VIB-KU Leuven, Belgium
saibar20 wrote:

Hello,

geNetClassifier is now updated and compatible with igraph 1.0.

It might take a few hours/a day for it to become available though. It will be ready to download/install when the version is updated to 1.8.1 (package page).

 

 

 

 

 

 

ADD COMMENTlink written 4.1 years ago by saibar20

Thank you.

Anita

ADD REPLYlink written 4.1 years ago by alakatos100
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