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Error when applying infer_network.jl on real experimental data #2

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Tianqi-Ma opened this issue May 27, 2020 · 0 comments
Open

Error when applying infer_network.jl on real experimental data #2

Tianqi-Ma opened this issue May 27, 2020 · 0 comments

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@Tianqi-Ma
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Tianqi-Ma commented May 27, 2020

Hi,
I am using infer_network.jl on experimental data (raw counts and log-transformed counts). But it returns error like this:

ERROR: LoadError: MethodError: no method matching setindex_shape_check(::Int64, ::Int64)
Closest candidates are:
setindex_shape_check(!Matched::AbstractArray{#s72,1} where #s72, ::Integer) at indices.jl:218
setindex_shape_check(!Matched::AbstractArray{#s72,1} where #s72, ::Integer, !Matched::Integer) at indices.jl:221
setindex_shape_check(!Matched::AbstractArray{#s72,2} where #s72, ::Integer, !Matched::Integer) at indices.jl:225
...
Stacktrace:
[1] macro expansion at ./multidimensional.jl:694 [inlined]
[2] _unsafe_setindex!(::IndexLinear, ::Array{Int64,1}, ::Int64, ::UnitRange{Int64}) at ./multidimensional.jl:689
[3] _setindex! at ./multidimensional.jl:684 [inlined]
[4] setindex! at ./abstractarray.jl:1020 [inlined]
[5] get_bin_ids!(::Array{Float64,1}, ::String, ::Int64, ::Array{Int64,1}) at /home/s4475694/.julia/packages/InformationMeasures/fdfJk/src/Discretization.jl:111
[6] Node(::Array{Any,2}, ::String, ::String, ::Int64) at /home/s4475694/.julia/packages/NetworkInference/z8pnG/src/common.jl:32
[7] #get_nodes#15(::Bool, ::String, ::String, ::Int64, ::Function, ::String) at /home/s4475694/.julia/packages/NetworkInference/z8pnG/src/infer_network.jl:35
[8] (::getfield(NetworkInference, Symbol("#kw##get_nodes")))(::NamedTuple{(:discretizer,),Tuple{String}}, ::typeof(get_nodes), ::String) at ./none:0
[9] top-level scope at util.jl:156
[10] include at ./boot.jl:326 [inlined]
[11] include_relative(::Module, ::String) at ./loading.jl:1038
[12] include(::Module, ::String) at ./sysimg.jl:29
[13] exec_options(::Base.JLOptions) at ./client.jl:267
[14] _start() at ./client.jl:436
in expression starting at /QRISdata/Q1851/Tianqi/GRN/scripts/infer_network.jl:31

However, there is no error when applying infer_network.jl on the simulated data you provided. BTW, I'm using Julia 1.1.1 in conda environment. The error is from:
@time genes = get_nodes(dataset_name);

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