ARACNE Manual

An Algorithm for the Reconstruction of Accurate Cellular Networks

Re: ARACNE Manual

Postby cwyoo » Thu Mar 12, 2015 4:02 pm

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:

Code: Select all
 
[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.
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Re: ARACNE Manual

Postby meninonas » Mon Mar 16, 2015 5:25 pm

Dr. Yoo,

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

Code: Select all
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.
Attachments
MasterFile.txt
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Re: ARACNE Manual

Postby cwyoo » Mon Mar 16, 2015 6:12 pm

meninonas wrote:Dr. Yoo,

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

Code: Select all
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).
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Re: ARACNE Manual

Postby meninonas » Tue Mar 17, 2015 3:07 pm

Dr. Yoo,

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

Code: Select all
aracne -i /Luis/Desktop/ARACNE/TestingFile1.txt


Code: Select all
aracne -i /Luis/Desktop/ARACNE/TestingFile2.txt


It gives me the same error:

Code: Select all
[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.
Attachments
TestingFile1.txt
(409 Bytes) Downloaded 158 times
TestingFile2.txt
(502 Bytes) Downloaded 154 times
meninonas
 
Posts: 137
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Re: ARACNE Manual

Postby meninonas » Thu Mar 19, 2015 11:09 am

Dr. Yoo,

I use the following command:

Code: Select all
aracne -i TestingFile2.txt


And got the following error:

Code: Select all
[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:

Code: Select all
aracne -i TestingFile2.txt

Code: Select all
aracne.exe -i TestingFile2.txt

Code: Select all
aracne2 -i TestingFile2.txt

Code: Select all
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.
meninonas
 
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Re: ARACNE Manual

Postby meninonas » Thu Mar 19, 2015 11:36 am

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

Code: Select all
aracne -i TestingFile2.txt


I got the following results:

Code: Select all
[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
Attachments
aracne.zip
(42.46 MiB) Downloaded 161 times
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Re: ARACNE Manual

Postby cwyoo » Thu Mar 19, 2015 11:38 am

meninonas wrote:Dr. Yoo,

I use the following command:

Code: Select all
aracne -i TestingFile2.txt


And got the following error:

Code: Select all
[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:

Code: Select all
aracne -i TestingFile2.txt

Code: Select all
aracne.exe -i TestingFile2.txt

Code: Select all
aracne2 -i TestingFile2.txt

Code: Select all
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.
cwyoo
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Re: ARACNE Manual

Postby meninonas » Thu Mar 19, 2015 1:37 pm

Dr. Yoo,

What do you mean the proper config_kernel?
Last edited by meninonas on Fri Mar 20, 2015 5:01 pm, edited 1 time in total.
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Re: ARACNE Manual

Postby cwyoo » Thu Mar 19, 2015 6:23 pm

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.
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