Import Table from file - blank rows in half of the data

[Max Gilbert]

Hello!

I have a problem with importing tables from files.

Basically it works correctly for 9/10 networks I visualize in Cytoscape, but once in a while I have an odd problem:

When improting table (e.g. protein attributes) to the network, it is only links half the data, while the other half is blank.

Usually I import tables as .txt or .csv filed and most of the time I dont run into that problem. Additionally, the import window shows the correct preview. I am absolutely sure that I use the correct key-column to map the data and I am absolutely sure that all of my data is represented in the table-file.

I included the files to this post.

I saw several topics with similar problems, but in these cases, it was mostly due to a corrupted table file or a wrong key column....im sure that this is not the case here since Cytoscape can assing around 50% of the values correctly.

Do you have a suggestion how to fix the problem?

Thanks a lot!

Cheers,

Max

[Max Gilbert]

hello again,

for the missing values, I made another screenshot to clarify: some nodes dont have a value in all columns, thats ok (red rectangles): https://i.imgur.com/yMoAIec.png

but some nodes dont have ANY values after importing the table, which is strange since I am absolutely sure they should at least have SOME values.

There was also no particiular error message in the task history: https://i.imgur.com/LiQ1n2W.png

but it seems like it stops at "loading..."?

max

[Scooter Morris]

Hi Max,

   Can you give us an example of a protein that should have values but doesn't?  I'm imported your data and just spot-checking, all of the ones I looked at actually don't have any values at all.

-- scooter

[Max Gilbert]

Hello Scooter,

Thanks for the reply!

In my second message, I posted some screenshots to illustrate my problem.

Here you can see, that cytoscape fails to assing values to certain proteins, while it works out fine to some others: https://i.imgur.com/yMoAIec.png

The screenshot corresponds to the files I uploaded to the original post.

So for example, AT1G77590 should have a value in column "DESCRIPTION"...but its not importet.

In my files, EVERY protein should have at least values for column "DESCRIPTION" (and others e.g. Mapman, BIN, Suba)

Its pretty strange, that in your case, NO protein has a value at all.

Is there something wrong with my file?

thanks,

Max

[Scooter Morris]

Hi Max,

   When I import your data, while every protein does have a DESCRIPTION field, many don't have the numeric values.  I thought that's what you were concerned with.  I've attached the session file I get from importing your data.

-- scooter

[Max Gilbert]

Hi Scooter,

Thanks a lot.

So that confirms that my Cytoscape is somehow broken....with the exact same files I provided here, I get a different result from yours.

Since you dont have a problem with my files at all, I guess, there isnt much I can do at this point and the problem is with my cytoscape or java.

I also tried reinstalling but it didnt help. Mysterious!

Cheers,

Max