SMLG (Statistical Machine Learning Group) Discussion Forum

meninonas wrote:Dr. Yoo,

I've been able to get the correct command for inputting the data into ARACNE. Nevertheless, I get the following error:

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[PARA] InputFile:     /luis/Downloads/MasterFile.txt
[PARA] Output File:
[PARA] Algorithm:     fixed_bandwidth 
[PARA] Kernel width:  determined by program
[PARA] MI P-value:    1
[PARA] DPI Tolerance: 1
Bad File
Problem with reading the file.


I've been playing around with the file setup to make sure it matches the one with the manual you provided. I'll continue on Monday.

Please upload the dataset that you used here and what you typed in to the command prompt to get the above message.

Dr. Yoo,

As you requested, please find the dataset attached. In addition, the command I used is the collowing:

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aracne -i /Luis/Desktop/ARACNE/MasterFile.txt

As the Manual requested, I saved it as a Tab Delimited File and formatted the excel sheet with two IDs as it requires two Column Headers as shown in the manual. I would suggest opening the file with Excel, as it is easier to see.

meninonas wrote:Dr. Yoo,

As you requested, please find the dataset attached. In addition, the command I used is the collowing:

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aracne -i /Luis/Desktop/ARACNE/MasterFile.txt

As the Manual requested, I saved it as a Tab Delimited File and formatted the excel sheet with two IDs as it requires two Column Headers as shown in the manual. I would suggest opening the file with Excel, as it is easier to see.

The manual clearly states the following:

"By convention, ARACNE inputs can be represented as tables where rows represent variables (e.g. ProbeSets in Affymetrix GEP dataset) and columns represent samples or observations (e.g. a single microarray experiment). There is one general rule that applies to all the entries in the table: no TAB character should be contained in any entry, because it will cause parsing problems to the program."

First, transpose your data and proceed. For testing purpose, you may just use ten variables with five samples (or cases).

Dr. Yoo,

I have run the following two commands with the attached datasets:

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aracne -i /Luis/Desktop/ARACNE/TestingFile1.txt

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aracne -i /Luis/Desktop/ARACNE/TestingFile2.txt

It gives me the same error:

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[PARA] InputFile:     /luis/Downloads/TestingFile1.txt
[PARA] Output File:
[PARA] Algorithm:     fixed_bandwidth 
[PARA] Kernel width:  determined by program
[PARA] MI P-value:    1
[PARA] DPI Tolerance: 1
Bad File
Problem with reading the file.

Dr. Yoo,

I use the following command:

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aracne -i TestingFile2.txt

And got the following error:

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[PARA] InputFile:     TestingFile2.txt
[PARA] Output File:
[PARA] Algorithm:     fixed_bandwidth 
[PARA] Kernel width:  determined by program
[PARA] MI P-value:    1
[PARA] DPI Tolerance: 1

[READ] 0 Description lines bypassed.
[READ] P-value columns not found.
Marker No: 9 <9 active>, Array No: 9
Cannot find file: ./config_kernel.txt! Please use '-N' option to specify the ARACNE home directory.

By the way, I got the same error when I used the following commands:

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aracne -i TestingFile2.txt

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aracne.exe -i TestingFile2.txt

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aracne2 -i TestingFile2.txt

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aracne2.exe -i TestingFile2.txt

So I don't believe that using the .exe file or having the 2 next to aracne makes a significant impact.

Dr. Yoo,

By downloading the aracne.zip file, which is in the Wikipedia page and on here, you'll find the config_kernell.txt file that Command Prompt requires.

Once I downloaded the zipped file, I ran the following command

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aracne -i TestingFile2.txt

I got the following results:

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[PARA] InputFile:     TestingFile2.txt
[PARA] Output File:
[PARA] Algorithm:     fixed_bandwidth 
[PARA] Kernel width:  determined by program
[PARA] MI P-value:    1
[PARA] DPI Tolerance: 1

[READ] 0 Description lines bypassed.
[READ] P-value columns not found.
Marker No: 9 <9 active>, Array No: 9
Kernell width determined for this dataset: 0.309707
10%, time: 0
20%, time: 0
30%, time: 0
40%, time: 0
50%, time: 0
60%, time: 0
70%, time: 0
80%, time: 0
90%, time: 0
Gene: 0 Time: 0
Writing matrix: TestingFile2_k0.31.adj

meninonas wrote:Dr. Yoo,

I use the following command:

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aracne -i TestingFile2.txt

And got the following error:

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[PARA] InputFile:     TestingFile2.txt
[PARA] Output File:
[PARA] Algorithm:     fixed_bandwidth 
[PARA] Kernel width:  determined by program
[PARA] MI P-value:    1
[PARA] DPI Tolerance: 1

[READ] 0 Description lines bypassed.
[READ] P-value columns not found.
Marker No: 9 <9 active>, Array No: 9
Cannot find file: ./config_kernel.txt! Please use '-N' option to specify the ARACNE home directory.

By the way, I got the same error when I used the following commands:

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aracne -i TestingFile2.txt

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aracne.exe -i TestingFile2.txt

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aracne2 -i TestingFile2.txt

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aracne2.exe -i TestingFile2.txt

So I don't believe that using the .exe file or having the 2 next to aracne makes a significant impact.

It is always a good idea to name the programs differently if they are in the same directory. In your directory, there were java execuable and windows executable with the same name.

Search and get the proper config_kernel.txt and move things forward.

Dr. Yoo,

What do you mean the proper config_kernel?

meninonas wrote:Dr. Yoo,

What do you mean the proper config_kernel? I wouldn't be able to tell what the correct kernel would look like.

To make sense of the results, that''s what needs to be researched. That is what research is all about: making sense of things that you were not able to understand.