error in values network files

[Leena Yadav]

Hi,
I am using cytoscape 3.3.0 and I am importing network from .xlx excel table. Numerical value of 1 imported fine but it gives me error:invalid number for the numerical values such as 0.99, 0.76 so on... When I click on error containing cell it shows that value is "0.99" whereas in my excel table they all are in like 1 or 0.99 or 0.76 so on ..therefore I have no idea why cytoscape recognise them like "0.99".
Please help me if this is a formatting issue or import issue.

Regards
Leena

[Scooter Morris]

Hi Leena,
   In the import dialog, you can click on the column header and tell Cytoscape that the column is a Floating Point column (click on the 1.0 button).  That will force the importer to read the data as floating point.

-- scooter

[Barry Demchak]

Leena –

 

We’d like to take a closer look at your input file … Cytoscape really should do this automatically.

 

Is there a version of your file that you can send us??

 

Thanks!

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

[Scooter Morris]

Hi Leena,
    I didn't have any problems importing your data.  Looks like a nice AP/MS data set!

-- scooter

On 1/14/16 10:54 PM, Leena Yadav wrote:

Hi Barry,
Thanks for your answer...
I have tried changing header to Floating Point column (click on the 1.0 button). also infact other options too ...but I still shows this error message.
I am also attaching a copy of excel table that i have used to do all this ... (error appear in several columns such as "saint score", Avg.P etc...)
Please help me in figuring out this.

Thanks once again.
Regards
Leena

On Thursday, January 14, 2016 at 5:55:36 PM UTC+2, Barry Demchak wrote:

Leena –

 

We’d like to take a closer look at your input file … Cytoscape really should do this automatically.

 

Is there a version of your file that you can send us??

 

Thanks!

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Scooter Morris
Sent: Thursday, January 14, 2016 7:40 AM
To: cytoscape-helpdesk
Subject: [cytoscape-helpdesk] Re: error in values network files

 

Hi Leena,
   In the import dialog, you can click on the column header and tell Cytoscape that the column is a Floating Point column (click on the 1.0 button).  That will force the importer to read the data as floating point.

-- scooter

On Thursday, January 14, 2016 at 6:18:21 AM UTC-8, Leena Yadav wrote:

Hi,
I am using cytoscape 3.3.0 and I am importing network from .xlx excel table. Numerical value of 1 imported fine but it gives me error:invalid number for the numerical values such as 0.99, 0.76 so on... When I click on error containing cell it shows that value is "0.99" whereas in my excel table they all are in like 1 or 0.99 or 0.76 so on ..therefore I have no idea why cytoscape recognise them like "0.99".
Please help me if this is a formatting issue or import issue.

Regards
Leena

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

[Barry Demchak]

Thanks, Lena … we’ll take a look at this shortly. This is a big help.

 

From: cytoscape...@googlegroups.com [mailto:cytoscape...@googlegroups.com] On Behalf Of Leena Yadav
Sent: Thursday, January 14, 2016 10:55 PM
To: cytoscape-helpdesk
Subject: Re: [cytoscape-helpdesk] Re: error in values network files

 

Hi Barry,
Thanks for your answer...
I have tried changing header to Floating Point column (click on the 1.0 button). also infact other options too ...but I still shows this error message.
I am also attaching a copy of excel table that i have used to do all this ... (error appear in several columns such as "saint score", Avg.P etc...)
Please help me in figuring out this.

Thanks once again.
Regards
Leena

On Thursday, January 14, 2016 at 5:55:36 PM UTC+2, Barry Demchak wrote:

[Barry Demchak]

Hi, Leena ... 

I didn't have any problem importing your spreadsheet either. I set the source node to Preditor and the target node to Prey, left the Interaction as interaction type, and everything else as edge attributes. 

I'm attaching the resulting .cys in case it's helpful to you.

Would you mind executing the Troubleshooting script and sending us the results? http://www.cytoscape.org/troubleshooting.html

Also, if there's a different assignment of values (e.g., as node attributes) you'd like us to try, please let us know.

In the meantime, I'll bring in a third set of eyes for this.

Thanks.

On Thu, Jan 14, 2016 at 10:54 PM, Leena Yadav <leen...@gmail.com> wrote:

Hi Barry,
Thanks for your answer...
I have tried changing header to Floating Point column (click on the 1.0 button). also infact other options too ...but I still shows this error message.
I am also attaching a copy of excel table that i have used to do all this ... (error appear in several columns such as "saint score", Avg.P etc...)
Please help me in figuring out this.

Thanks once again.
Regards
Leena

On Thursday, January 14, 2016 at 5:55:36 PM UTC+2, Barry Demchak wrote:

--

vvvvvvvvvvvvvvvvvvvvvvvvvvvv
: Barry Demchak, PhD
: UC San Diego, Department of Medicine
: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home
: (858) 452-8700
vvvvvvvvvvvvvvvvvvvvvvvvvvvv

[Leena Yadav]

Hi Barry and Morris,
I run the troubleshooting script and it seems I have to manually change the settings for several column (in which I had errors in beginning)!!
I opened the file that you have attached and still have errors but if I change manually (Floating point to 1.0 type) then i get them all there.I thought cytoscape should do that automatically for all columns but it is not.

Regards
Leena

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpdesk+unsub...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

[Barry Demchak]

Hi, Leena –

 

Would you mind sending us the results of the troubleshooting script?

 

Also, when you say you had to manually change the settings for several columns, what were the original settings, and what did you change them to?

 

Are you reporting that you had errors opening the .cys file I sent you? … which columns did you manually change?

 

Cytoscape should be importing data automatically. We need more precise information so we can understand exactly what you’re reporting, so then we can determine what the proper behavior is.

 

Thanks.

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

 

--

vvvvvvvvvvvvvvvvvvvvvvvvvvvv
: Barry Demchak, PhD
: UC San Diego, Department of Medicine
: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home
: (858) 452-8700
vvvvvvvvvvvvvvvvvvvvvvvvvvvv

--

You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.

To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

[Guilherme Juvenal]

Hello, my name is Guilherme and I'm having the same problem as above: Error when evaluating an equation: Invalid value.

I already followed all the steps above, marking a column as float, I tried to enter data in several ways until using previous versions of cytoscape, but I was not successful in adding data related to edge weighting.

Can you help me?

[Scooter Morris]

Hi Guilherme,

These sound like two different errors.  It sounds like you are using an equation and using the output of the equation as a weight, is that correct?  As with Leena, we would need to see the exact input and the equation your are using, but an off-hand guess would be that you are trying to run an equation on a missing field.  If you can send us that data, we would be happy to take a look.

-- scooter

[Ági G]

Hi, 

I had the same problem as Leena. I converted .xls file into .csv file and the problem was solved. 

Hope this helps others with the same issue.

Agnes

[Sandra Alday]

Hello, when I try to import a network from table (.CSV file) with a column containing large values (imported as long integers), Cytoscape converts the large values to 1.

Could I please request for help with this error? Thanks!

[Alex Pico]

Hi Sandra,

Can you provide the CSV or a small sample of the file, so that we can reproduce the issue?

[Sandra Alday]

Thanks Alex! Here it is (enclosed)

 

From: 'Alex Pico' via cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Wednesday, 2 February 2022 12:07 PM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: Re: [cytoscape-helpdesk] Re: error in values network files

 

Hi Sandra,

 

Can you provide the CSV or a small sample of the file, so that we can reproduce the issue?

 

--

You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/290cde7d-4822-4fcf-8e5c-925f544294e4n%40googlegroups.com.

[Alex Pico]

Thanks. The values imported just fine. See my screenshot for how I picked the import settings. Note that column E in your spreadsheet is missing a header, but it still imports fine.

Here are the steps I did:

1. File > Import > Network from file...

2. Choose your CSV

3. Network collection: --- Create new network collection ---

4. Set "source", "interaction" and "target" for first 3 columns

5. Set "edge attribute" for others

6. Click OK

Can you describe the steps you are doing?

[Alex Pico]

screenshot

[Sandra Alday]

Thanks Alex, I’d like to manipulate target node size to reflect USD mn. Could you please try to import the USD mn column as target node attribute and see what you get? Many thanks!

 

From: 'Alex Pico' via cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Wednesday, 2 February 2022 12:23 PM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: Re: [cytoscape-helpdesk] Re: error in values network files

 

screenshot

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/fe1c3757-ab17-47ca-bd3f-0a33db59570cn%40googlegroups.com.

[Alex Pico]

Oops! I spoke to soon. Cytoscape is actually performing correctly.

If you look at your data in Excel, you'll see that you have multiple values of USD mn per target "Partner." So, what value would you expect in the Node Table?  Cytoscape imports each row and maps the value to the node. The last value mapped is 1 (as it is in your table), so that's the one that you see after import is complete.

[Alex Pico]

So, the solution is to only have one value of USD mn per partner. Or if you want the maximum, then sort your table by USD mn prior to importing. If you want minimum, then that is what you are currently getting, i.e., the minimum is 1 for each of the partners.

[Sandra Alday]

Ah yes that sounds like the fix! Thanks Alex.

Get Outlook for iOS

---

From: 'Alex Pico' via cytoscape-helpdesk <cytoscape...@googlegroups.com>

Sent: Thursday, February 3, 2022 7:11:08 AM

To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: Re: [cytoscape-helpdesk] Re: error in values network files

So, the solution is to only have one value of USD mn per partner. Or if you want the maximum, then sort your table by USD mn prior to importing. If you want minimum, then that is what you are currently getting, i.e., the minimum is 1 for each of the partners.

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/5dffced8-f6a7-46df-9b89-db6a8fefd69dn%40googlegroups.com.

[Sandra Alday]

Sorry for spamming Alex. One more question - if I consolidate all the values for the target nodes so that there’s only one value per node, then I’m going to lose edge count data. 

I don’t want to lose either data point. Is there a way to preserve both?

Get Outlook for iOS

---

From: 'Sandra Alday' via cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Thursday, February 3, 2022 7:58:08 AM
To: cytoscape...@googlegroups.com <cytoscape...@googlegroups.com>

Subject: Re: [cytoscape-helpdesk] Re: error in values network files

Ah yes that sounds like the fix! Thanks Alex.

Get Outlook for iOS

---

From: 'Alex Pico' via cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Thursday, February 3, 2022 7:11:08 AM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: Re: [cytoscape-helpdesk] Re: error in values network files

 

So, the solution is to only have one value of USD mn per partner. Or if you want the maximum, then sort your table by USD mn prior to importing. If you want minimum, then that is what you are currently getting, i.e., the minimum is 1 for each of the partners.

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/5dffced8-f6a7-46df-9b89-db6a8fefd69dn%40googlegroups.com.

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/SYCPR01MB45590BF65A7F0285CABE227EE8279%40SYCPR01MB4559.ausprd01.prod.outlook.com.

[Alex Pico]

Sure. Two approaches:

1. Replace all USD mn values with repeats of the same value per Partner, keeping all your original rows in your spreadhsheet. Cytoscape will simply overwrite the value as it reads each line and the last one will be kept (in the case of node attributes), while each edge will be kept.

2. Skip importing USD mn values when you import the network as a file. Then, in a subsequent step, import a separate, simpler table containing just the Partners and USD mn values as node attributes.

[Sandra Alday]

Thanks Alex, will try that out.

 

From: 'Alex Pico' via cytoscape-helpdesk <cytoscape...@googlegroups.com>
Sent: Thursday, 3 February 2022 9:11 AM
To: cytoscape-helpdesk <cytoscape...@googlegroups.com>
Subject: Re: [cytoscape-helpdesk] Re: error in values network files

 

Sure. Two approaches:

 

1. Replace all USD mn values with repeats of the same value per Partner, keeping all your original rows in your spreadhsheet. Cytoscape will simply overwrite the value as it reads each line and the last one will be kept (in the case of node attributes), while each edge will be kept.

2. Skip importing USD mn values when you import the network as a file. Then, in a subsequent step, import a separate, simpler table containing just the Partners and USD mn values as node attributes.

 

--

You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/eda99f2b-c4f4-4639-9d28-7e8969cb07cbn%40googlegroups.com.