Format of a background file

[ychi...@gmail.com]

Hi,

I am analysing expression data using a background file that contains a list of non-expressors.

1)When I upload  a datafile and with expression levels and P-values and the default background settings, egan recognized this file just fine

(here is the format of the file. I am using HUGO gene names for mapping)

#!Expression. Feature ID Dex UP-Difference P-value

Ddit4         4.56 0.000336

Dusp 1 3.34 9.78E-04

Tsc22d3 3.33 0.0012

2) When I upload a background file (in the same format) pretending that it is a datafile, Egan also recognizes it just fine

3) However, when I tried to substitute the background file with mine  Egan terminates with the Error Message below

java.lang.Exception: No Entrez Gene nodes in network. Check to see that identifier mapping files are correct.

at edu.ucsf.cc.icore.app.egan.launch.DataControllerFactory.constructDataController(DataControllerFactory.java:151)

at edu.ucsf.cc.icore.app.egan.launch.LaunchEganThread.run(LaunchEganThread.java:119)

at java.lang.Thread.run(Unknown Source)

It seems that the format for a background file should be different, but in what way?

[ucsf egan]

Hello,

Thanks for posting. I can see two problems (it's likely the first)

The # symbol is a controlled character that identifies comment lines
in most EGAN files. Give it a try without the #!

Also, you would have problems if you're using Mouse data with Human
EGAN, for example.

Good luck,

Jesse

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[ychi...@gmail.com]

Removing the comment line didn't change a thing. The same error. I tried it in several combinations. Basically, when I use any of my expression files with the default background Egan recognizes them and analyze properly. Only when I try to use the same files as Background files it  produces this error message. So the question then is in what format a background file supposed to be? Do you have an example of a working background file?

[ucsf egan]

Ah, I see now.  The background file is a different format from the experiment.  It's the same format as a mapping file.  Tab-delimited text, with 3 columns.   The first column is your experiment ID, the second column is null, and the third column is an Entrez Gene ID.  The tutorial document http://akt.ucsf.edu/EGAN/docs/EGAN_tutorial_Loading_experiment_results.pptx might help.

Best,

Jesse

[nsl]

Hi, I ran into the same problem with regard to uploading a background file. Did Jesse's suggestions about formatting the background file similar to the mapping file work for you?

sincerely

nsl