Package "geNetClassifier": is this an "igraph' error?
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alakatos ▴ 130
@alakatos-6983
Last seen 5.2 years ago
United States

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 
 

>

 
software error geNet igraph genetclassifier • 2.3k views
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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.

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Thank you.

Anita

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saibar ▴ 20
@saibar-7798
Last seen 6.5 years ago
University of Salamanca, Spain / VIB-KU…

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).

 

 

 

 

 

 

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Thank you.

Anita

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