Entering edit mode
                    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:
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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)
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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.
Thank you.
Anita