[cytoscape-helpdesk] trouble importing text file with node attributes

[Stephen Bonasera]

Hi all,

I just received some gene expression data from the UCSF LB core, and I
am having some trouble with my usual workflow. I have no problem
making a literature based interaction network using the Agilent
plugin. My trouble is importing the node attributes (most importantly,
FDR values for the each node, as well as symbol name, etc.). The data
is in a large .txt file (like I used to do it). I'm using 2.6.3 on OS
X 10.5.8, with the most recent Java update. I use file->import-
>attribute from table, select my file, then check the following boxes:

Attributes - node
Import file name - ...
Show mapping options
Show text file import options
Import everything (key ...)
(I don't check case sensitive)

Delimiter is tab
Transfer first line as attribute names

I switch the ID to gene symbol, and that column does turn blue
All the other columns have a check mark at their top, remain black

I do see the data and the other node attributes

When I hit import, I get the window saying it loads, and then the
following message:

Succesfully loaded attribute data from:

file:/Users/sjb/Desktop/mBALBcerebYngOld.txt

41174 entries are loaded and mapped onto
NODE attributes.

The following enties are invalid and were not imported:
4931419H13Rik =
Phkb =
Eppk1 =
2310050B05Rik =
Kcng2 =
Tspan18 =
LOC383707 =
5230400M03Rik =
1110014L15Rik =
Cyfip2 =
Ankfy1 =
Approximately 8576 additional entries were not imported...

Here's the rub. While cytoscape has the node attribute names now
imported, no data is present in any of the attributes.

Thanks so much for thinking about this. I've spent the morning trying
all sorts of modifications (only two column imports, checking
different options) with no progress.

Cheers,

Steve Bonasera

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[Scooter Morris]

Hi Stephen,
Looks like those "=" signs shouldn't be there. Can you send a copy
of your text file directly to me? I can take a look at it and try to
figure out what's going on.

-- scooter