how to export BINGO table

[Elvira Inglese]

Hi, I I've a question about the result table after enrichment GO analysis with BINGO:

How can I export this table as txt? or save this resut into cytoscape session? 

regards, 

Elvira

[Tim Hull]

To save the file, check the box at the bottom of the BiNGO settings panel and select an output directory using the "Save BiNGO Data File..." button. If you run the analysis after doing that, it will save the output as <name>.bgo in the selected directory (where name is the cluster name specified at the top of the dialog).

Unfortunately, you can't save the output *after* running the analysis - you have to select this in the settings before doing so.

Hope this helps...

Tim

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[Elvira Inglese]

thank you so much! 

Elvira

2014-01-29 Tim Hull <tmh...@eng.ucsd.edu>

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[karl.f...@gmail.com]

Hello Tim,

I'm trying to save BiNGO output upon running the program, but I get the following error when I try to run:

"Data File:  FILE NAMING ERROR:  java.io.FileNotFoundException:  /ChIP_analysis/B5f.bgo (No such file or directory)

I'm not sure what I'm doing wrong here.  "B5f" here is the cluster name I've specified at the top of the BiNGO Settings window.  I can't appear to just select an output directory when I click the "Save BiNGO Data File in:" button, it forces me to enter something in the box, so I enter "B5f".

Thanks in advance if you know how to fix this!

Best,

Karl

[Tim Hull]

You're not supposed to enter a file name - just open the directory you want to save in and press "Save" to save in that directory. Then it should work...

Tim

For more options, visit https://groups.google.com/d/optout.

[karl.f...@gmail.com]

Hi Tim,

Thanks for getting back to me.  That is exactly the problem, I'm not able to just open the directory and press "Save".  If I double-click on a directory - say "Desktop" - to select it, then the word "Desktop" appears in the Save As text box.  If I delete the word "Desktop" in the Save As text box, then the Save button at the bottom is de-activated.  I've attached a screen shot to illustrate what I'm referring to.

Best,

Karl

[karl.f...@gmail.com]

Forgot the screenshot:

[Tim Hull]

The image didn't come through - just a bunch of gibberish, and I was unable to convert it to an image. In any case, you shouldn't have to delete the file name - just pressing save after double-clicking the directory you want to open it should be enough.

Tim

[karl.f...@gmail.com]

Hi Tim,

Sorry about the failed screenshot, though I don't think it would've helped anyway.  Unfortunately the problem remains if I follow your directions and just press Save after double-clicking on a directory.

Here's the error message I get when I press Save after double-clicking the directory "MartinLabStuff" I want to save the file to:

Data File:  FILE NAMING ERROR:  java.io.FileNotFoundException:  /Users/karlerhard/MartinLabStuff/MartinLabStuff/B5f.bgo (No such file or directory)

In this case, the cluster name is called "B5f".

As you can see, upon pressing the Save button, the program seems to be creating an additional folder called "MartinLabStuff" that doesn't actually exist.  I believe this is causing the problem, and it happens no matter what directory I try to open.

Hope that clarifies the problem.

Thanks for continuing to try to help!  Sorry if I haven't been describing the issue correctly.

Karl

[Tim Hull]

I do think it would help - it sounds like your OS'es Save As dialog box may be behaving differently than most. Could you try to post the screenshot again?

Tim

[karl.f...@gmail.com]

Hi Tim,

OK, here are a couple illustrative screenshots, one where I've just double-clicked on a directory, and one where I've deleted the "MartinLabStuff" in the Save As box, which shows the greyed out Save button at the bottom.  I'm attaching them instead of drag-and-dropping them into text box, hope that works.

Thanks,

Karl

[Tim Hull]

Have you tried single-clicking on the folder and pressing Save? On a Mac, it seems that double-clicking causes it to copy the folder's name twice...

Tim

[Seb ...]

Tim

although a bit late, you can go to "File" -> "export" -> "table" -> in "select table to export" pick the node table of the GO network created by BiNGO, it will save the ontology terms, p.values and a bunch of other things.

Seb