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Heat #3965: Add extra colum with GO info
Ellen Sterrenburg <E.sterrenburg@lumc.nl>
2003-04-23 07:49:51
Hi Chris,

Is it possible to add an extra column to the export table with the Gene
Annotation of the genes you're interested in? I know it is possible to
right-click your mouse and then have several options, also for annotation,
but is this also possible to have this information in a table for several
genes at once?

1) The gene annotation that I would like to export is the gene ontology. The
problem here is that you have 3 main functions:
Biological proces, Molecular function and Cellular component. And a second
problem is that there are different levels of these functions. Ideally I
would like to have all in different columns, but I don't know if that is
possible.
To give you an idea, what I do now is, I export the acc.nrs. of the genes I
am interested in (for intance significant in my ANOVA) and I load them into
eGOn. There you can upload a batch of acc.nrs. and get the ontology tree per
function. Here you can export an excel file and then you have a file with
the acc.nrs. with their functions. You understand that if this is possible
in Rosetta it would save a lot of time!

2) Where I would like to export it, is out of the cluster viewer. So that
you have a table with the genes you're interested in, their cluster number,
the ratio data and their function. After that it is easy to make pies per
cluster so that you can see if genes with one (or more) particular functions
fall into one cluster.


Hoi Ellen,

There is a way to add custom columns to the Matrix Viewer and then be able
to export the custom columns along with the cluster number and ratio data.
It will take a little work to describe and perform so I have included a Word
document with screen shots for ease. Let me know if it helps and if I can
close the case. Again this will require Resolver to be at the Version and
Build of 3.2.1.1.14.

Best,

Chris Dagsgaard

Document with screen shots is on: I:Lab-J:Rosetta Heat #3965


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Title
Author
Date
Heat 3287: flags in GenePix -> fail codes in Rosetta
Judith Boer
2003-03-03 12:04:44
Heat 3358: export data for several profiles/experiments ...
Judith Boer
2003-03-03 12:05:19
Heat 3288: import_gpr-profiles.txt
Judith Boer
2003-03-11 11:29:45
export-anova.txt
Judith Boer
2003-03-11 11:30:13
adding columns of gene annotation to expression data
Judith Boer
2003-03-11 11:31:33
only ~4000 UniGene clusters Affy chip U133A?
Judith Boer
2003-03-11 11:34:10
Heat 3573: Changing the scale of y-axis in trend plots
Ellen Sterrenburg
2003-03-12 16:47:55
problems with image view
Peter-Bram 't Hoen
2003-03-14 14:44:20
Re: problems with image view
Peter-Bram 't Hoen
2003-03-28 11:07:43
Re: problems with image view
Peter-Bram 't Hoen
2003-03-28 11:46:50
Re: problems with image view
Ellen Sterrenburg
2003-04-03 17:56:18
dealing with flags
Peter-Bram 't Hoen
2003-03-14 15:33:43
do not use dashes in chip names!
Peter-Bram 't Hoen
2003-03-28 11:09:53
importing gpr files
Peter-Bram 't Hoen
2003-03-28 11:44:33
Re: importing gpr files
Ellen Sterrenburg
2003-04-03 17:54:08
Dye-swaps and combining hybs
Ellen Sterrenburg
2003-04-04 16:09:04
Importing a whole list of Acc. # to create a bioset
Ellen Sterrenburg
2003-04-09 14:57:22
Use of self-self hybridization in an ANOVA
Ellen Sterrenburg
2003-04-09 14:59:47
Heat 3903: "stitch" together data of two chips ...
Ellen Sterrenburg
2003-04-10 11:46:34
Heat 3954: Determine the number of clusters for K-means ...
Ellen Sterrenburg
2003-04-15 17:35:41
Heat 3902: Clustering in trend viewer
Ellen Sterrenburg
2003-04-15 17:39:28
Heat 3963: 1 table with cluster number and ratio data
Ellen Sterrenburg
2003-04-17 07:44:13
Heat #3965: Add extra colum with GO info
Ellen Sterrenburg
2003-04-23 07:49:51
Heat 4053:Select genes with signal in at least one exp. ...
Ellen Sterrenburg
2003-04-30 07:47:48
Heat 4211: Request for colored clusters from trend viewer
Ellen Sterrenburg
2003-06-17 07:42:37
Heat 4789:Spots with no signal
Ellen Sterrenburg
2003-07-11 11:21:19
Re: Heat 4789:Spots with no signal
Ellen Sterrenburg
2003-07-14 15:04:57
What to do before you load your profile?
Ellen Sterrenburg
2003-08-18 15:36:28
cell number
Peter-Bram 't Hoen
2003-08-27 17:07:29
image viewer - zoom in?
Peter-Bram 't Hoen
2003-08-27 17:10:25
polarity
Peter-Bram 't Hoen
2003-08-27 17:11:05
Correcting for multiple testing in Rosetta
Ellen Sterrenburg
2003-09-25 17:59:08
Q$A: How do you delete data from the system?
Anders
2003-10-22 10:11:08
Import Agilent pattern
Peter-Bram 't Hoen
2003-11-13 14:53:40
downregulated features that appear as upregulated
Peter-Bram 't Hoen
2003-11-13 14:55:50
Export data in Excel format
Ellen Sterrenburg
2004-01-27 12:27:06
Re: Export data in Excel format
Ellen Sterrenburg
2004-02-11 07:43:51
Plotting and exporting ANOVA results
Ellen Sterrenburg
2004-02-11 07:53:03
The export-values in the trend are always log10 values!!!! ...
Ellen Sterrenburg
2004-02-19 07:52:59
Log(error)
Ellen Sterrenburg
2004-04-15 17:57:37
Exporting high-quality figures for publications
Peter-Bram 't Hoen
2004-08-27 13:07:47
ANOVA in experiment defenition-multiple testing
Peter-Bram 't Hoen
2005-02-09 09:03:41
Combine-on-the-fly of experiments no longer possible
Peter-Bram 't Hoen
2005-04-13 10:21:54
Hainofaft

2009-01-13 21:07:52
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2011-01-17 11:30:46