Re: Need instructions for jActiveModules in Cytoscape 3.2.1

[Krupa]

As per the old instructions for jActiveModules listed here: http://wiki.cytoscape.org/Presentations/07_Complexes#Identify_perturbed_complexes_using_expression_data:_jActiveModules

the input required gene expression data as well as the p-values from the microarray data. In Cytoscape 2.x versions, gene expression data could be imported separately as follows: File → Import → Attribute/Expression Matrix.

In Cytoscape 3.2.1, is there a way to import gene expression data as an Expression Matrix?

Does jActiveModules in Cytoscape 3.2.1 only use the corrected p-values (ranging from 0 to 1) derived from the microarray data set or does it still need the normalized expression signal intensities as well?

Thanks,

Krupa

[Tim Hull]

To import expression data, just use the standard table import (File-Import-Table-File...). There is no separate Attribute/Expression Matrix option in Cytoscape 3.2.1.

jActiveModules can use any type of expression value - values not on a 0 to 1 scale will be normalized to that scale prior to processing.

Hope this helps...

Tim

--
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 http://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

[Krupa]

Thanks Tim! It makes sense now.

-Krupa

On Monday, 1 June 2015 12:47:23 UTC-7, Tim Hull wrote:

To import expression data, just use the standard table import (File-Import-Table-File...). There is no separate Attribute/Expression Matrix option in Cytoscape 3.2.1.

jActiveModules can use any type of expression value - values not on a 0 to 1 scale will be normalized to that scale prior to processing.

Hope this helps...

Tim

On Fri, May 29, 2015 at 3:22 PM, Krupa <nava...@gmail.com> wrote:

As per the old instructions for jActiveModules listed here: http://wiki.cytoscape.org/Presentations/07_Complexes#Identify_perturbed_complexes_using_expression_data:_jActiveModules

the input required gene expression data as well as the p-values from the microarray data. In Cytoscape 2.x versions, gene expression data could be imported separately as follows: File → Import → Attribute/Expression Matrix.

In Cytoscape 3.2.1, is there a way to import gene expression data as an Expression Matrix?

Does jActiveModules in Cytoscape 3.2.1 only use the corrected p-values (ranging from 0 to 1) derived from the microarray data set or does it still need the normalized expression signal intensities as well?

Thanks,

Krupa

--
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.

[Krupa Navalkar]

Hi ! Tim,

I have an input tab delimited text file that contains p-values ranging from 0 to 1 that I'm using as an input to jActiveModules. Once I load this file up, Whose column headers are as follows:

GENE COMMON Timepoint1 Timepoint2 etc... 

where, GENE = Entrez Gene ID

COMMON = Gene Symbol

Timepoint1 = corrected p-value from microarray data ranging from 0 to 1.

Once this file is loaded into Cytoscape, jActiveModules populates the node columns as follows:

GENE COMMON Timepoint1exp Timepoint1sig Timepoint2exp Timepoint2sig etc... 

Both exp and sig columns have the same values, do you know why it splits & duplicates input columns like this? In our previous conversation you mentioned the new jActiveModules takes p-values OR microarray intensities as input. I'm trying to obtain this information for a submission on Tuesday June 9th, 2015 next week and would really appreciate your help before then.

Thanks,

Krupa

On 1 June 2015 at 12:47, Tim Hull <tmh...@eng.ucsd.edu> wrote:

To import expression data, just use the standard table import (File-Import-Table-File...). There is no separate Attribute/Expression Matrix option in Cytoscape 3.2.1.

jActiveModules can use any type of expression value - values not on a 0 to 1 scale will be normalized to that scale prior to processing.

Hope this helps...

Tim

On Fri, May 29, 2015 at 3:22 PM, Krupa <nava...@gmail.com> wrote:

As per the old instructions for jActiveModules listed here: http://wiki.cytoscape.org/Presentations/07_Complexes#Identify_perturbed_complexes_using_expression_data:_jActiveModules

the input required gene expression data as well as the p-values from the microarray data. In Cytoscape 2.x versions, gene expression data could be imported separately as follows: File → Import → Attribute/Expression Matrix.

In Cytoscape 3.2.1, is there a way to import gene expression data as an Expression Matrix?

Does jActiveModules in Cytoscape 3.2.1 only use the corrected p-values (ranging from 0 to 1) derived from the microarray data set or does it still need the normalized expression signal intensities as well?

Thanks,

Krupa

--
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 http://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 a topic in the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/5Rnfcmrg36M/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.

[Krupa]

Hi ! Tim,

I have an input tab delimited text file that contains p-values ranging from 0 to 1 for jActiveModules within Cytoscape. The column headers of this input file are as follows:

GENE COMMON Timepoint1 Timepoint2 etc... 

where, GENE = Entrez Gene ID

COMMON = Gene Symbol

Timepoint1 = corrected p-value from microarray data ranging from 0 to 1.

Once this file is loaded into Cytoscape v3.2.1, jActiveModules populates the node columns as follows:

GENE COMMON Timepoint1exp Timepoint1sig Timepoint2exp Timepoint2sig etc... 

Both 'exp' and 'sig' columns have the same values, do you know why it splits & duplicates input columns like this when I've just given it p-values and no signal intensities? In our previous conversation you mentioned the new jActiveModules takes either p-values OR microarray intensities, not both simultaneously as input. I look forward to your guidance.

Thanks,

Krupa

On Monday, 1 June 2015 12:47:23 UTC-7, Tim Hull wrote:

To import expression data, just use the standard table import (File-Import-Table-File...). There is no separate Attribute/Expression Matrix option in Cytoscape 3.2.1.

jActiveModules can use any type of expression value - values not on a 0 to 1 scale will be normalized to that scale prior to processing.

Hope this helps...

Tim

On Fri, May 29, 2015 at 3:22 PM, Krupa <nava...@gmail.com> wrote:

As per the old instructions for jActiveModules listed here: http://wiki.cytoscape.org/Presentations/07_Complexes#Identify_perturbed_complexes_using_expression_data:_jActiveModules

the input required gene expression data as well as the p-values from the microarray data. In Cytoscape 2.x versions, gene expression data could be imported separately as follows: File → Import → Attribute/Expression Matrix.

In Cytoscape 3.2.1, is there a way to import gene expression data as an Expression Matrix?

Does jActiveModules in Cytoscape 3.2.1 only use the corrected p-values (ranging from 0 to 1) derived from the microarray data set or does it still need the normalized expression signal intensities as well?

Thanks,

Krupa

--
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.

[Tim Hull]

Do these exp and sig columns exist at all in the data you imported? Do they exist in the Cytoscape node table before you run jActiveModules? jActiveModules shouldn't create any new columns, so I'm not sure how they would get there...

Tim

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 http://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.

[Krupa]

No Tim. These exp and sig column label's don't exist in my input data. When I import a node table through Cytoscape, jActiveModules adds these suffixes to the end of column names I've provided in the input file and duplicates my original input columns to add the exp and sig suffixes to the end of every column name. You could try it if you like using the Nature Protocols Cytoscape paper example .sif and .pvals sample files. Or let me know and I could send them to you.

Thanks for your prompt response.

Sincerely,
Krupa

---

From: Tim Hull
Sent: ‎6/‎5/‎2015 6:16 PM
To: cytoscape...@googlegroups.com
Subject: Re: [cytoscape-helpdesk] Re: Need instructions for jActiveModules inCytoscape 3.2.1

You received this message because you are subscribed to a topic in the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/cytoscape-helpdesk/5Rnfcmrg36M/unsubscribe.
To unsubscribe from this group and all its topics, send an email to cytoscape-helpd...@googlegroups.com.

[Krupa]

Hi ! Tim,

These duplicate columns show up in the node table browser and not during the import table dialog. They also show up in the jActiveModules column selection pane on the left after being imported. The sample files are attached to this e-mail from the article:

1.      Integration of biological networks and gene expression data using Cytoscape. Melissa Cline, Ilya Shmulevich, Trey Ideker et al. Nat Protoc. 2007; 2(10): 2366-2382. doi:10.1038/nprot.2007.324.

Link for paper supplement: http://www.nature.com/nprot/journal/v2/n10/suppinfo/nprot.2007.324_S1.html#browser-plugins

I'm importing the .sif file as follows: File-> Import-> Network -> File

Importing the .pvals file as follows: File-> Import->Table->File

The original .pvals file included in the Nature Protocols example is: galExpData_original.pvals

It includes both the microarray data as well as columns containing the p-values. I've edited this file to only include p-values, filename: galExpData_Edited.pvals

If you load the galExpData_Edited.pvals file, the problem of column duplication occurs with one set of data columns being given the suffix 'sig' and another set with suffix 'exp' added to it as displayed in the node table browser. I've included a Cytoscape session file in the .zip file so you could see this if you have jActiveModules installed within Cytoscape v3.2.1 filename: galExpData_Edited_Session_Example.cys

If you load the original file containing both p-values and microarray expression values (galExpData_original.pvals), the columns are not duplicated and automatically, the microarray data columns take on the 'exp' suffix and the p-value columns take on the 'sig' suffix. I tried doing this with my data, using both p-values and microarray signal intensities, but the 'exp' and 'sig' suffixes were not appended in that order.

This was why I had originally asked you when selecting which column of data to derive the activated network from using jActiveModules, should one select the p-values or microarray signal intensities or both per timepoint (I have longitudinal data)?

Thank you so much for your time and effort. I really look forward to your guidance. Many Thanks!

Sincerely,

Krupa

[Tim Hull]

It seems that by using the .pvals extension, your data is being imported by a special Expression Matrix importer, similar to the one you would use in 2.8.x. However, since you only have p-values, your data doesn't fit that format - chance why you're getting the duplicate columns. If you rename to something else (i.e. .tsv), you should be able to import as a generic tab-separated table and not get multiple columns.

Hope this helps...

Tim

[Krupa]

Thank you Tim! It worked! This is perfectly in time for my submission, so really appreciate your kind gesture!

As per your instructions, I just saved the file as a tab delimited text file instead of with the ".pvals" extension. While importing the microarray p-values table, I changed the primary identifier column type to "string" format to match the default format for "shared name" (string) although my primary identifier was numerical and it worked!

Thanks so much for your help.

Sincerely,

Krupa

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