AMARETTO Results

[Srinathkandalam]

Hello

I tried run AMARETTO which was given in google collab for the already processed data and followed the same exact steps [https://colab.research.google.com/drive/1JfnRoNgTVX_7VEGAAmjGjwP_yX2tdDxs#scrollTo=1XemfQskXI2N].

I had the following error in the results section. Please help me out.

Code:
MA_matrix_LIHC = read_gct("https://datasets.genepattern.org/data/module_support_files/Amaretto/TCGA_LIHC_Expression.gct")
CNV_matrix_LIHC = read_gct("https://datasets.genepattern.org/data/module_support_files/Amaretto/TCGA_LIHC_CNV.gct")
MET_matrix_LIHC = read_gct("https://datasets.genepattern.org/data/module_support_files/Amaretto/TCGA_LIHC_Methylation.gct")
ProcessedData_LIHC = list(MA_matrix=MA_matrix_LIHC, CNV_matrix=CNV_matrix_LIHC, MET_matrix=MET_matrix_LIHC)
data("Driver_Genes")
TF_candidate_drivers <- Driver_Genes$TFs_TFutils_union

combination_method <- "union"
NrModules = 150
VarPercentage = 75
NrCores = 4
AMARETTOinit <- AMARETTO_Initialize(ProcessedData = ProcessedData_LIHC,
Driver_list = TF_candidate_drivers,
method = combination_method,
NrModules = NrModules,
VarPercentage = VarPercentage,
NrCores = NrCores)
AMARETTOresults <- AMARETTO_Run(AMARETTOinit = AMARETTOinit)

Error
Found 734 CNV driver genes.
Found 1816 MethylMix driver genes.
Found 947 driver genes from the input list.
Found a total of 3177 unique drivers with your selected method.

AMARETTOresults <- AMARETTO_Run(AMARETTOinit = AMARETTOinit)
Running AMARETTO on 11180 genes and 367 samples.
Stopping if less then 111.8 genes reassigned.
Autoregulation is turned ON.
Error in dimnames(x) <- dn :
length of 'dimnames' [2] not equal to array extent
In addition: Warning message:
In (function (..., deparse.level = 1) :
number of rows of result is not a multiple of vector length (arg 1)