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Heat 3287: flags in GenePix -> fail codes in Rosetta
Judith Boer <j.m.boer@lumc.nl>
2003-03-03 12:04:44
Hoi Judith

I'm still working on this but I wanted to share with you what I've been
working on.

I was investigating the fail codes with the .gpr profile from you that I
loaded and I can see that the software does differentiate between the -50
and -100 fail codes.

What I did was select the Ratio Experiment that I had loaded and viewed the
table of sequences for that experiment. To see all the flagged sequences in
the experiment, go to the 'Groups' menu and select 'Flagged|Show' (you might
also want to select 'Flagged|Hide Others'). In this table is a column
called 'Fail Code(s). The entries in the .gpr file that have a -50 code
appear with the description "No Signal(Green), No Signal(Red)" and the
entries with -100 have "Software Flagged".

What I am still working on is the best way to use this information to get
what you are looking for. From a feature level table (or from the Image
Viewer), the 'admin' can right-click on a feature and flag it as bad but,
ideally, you want to use the information that is already there to do this.
I also want to investigate what the implications of each 'Fail Code' is on
the data analysis.

Anyway, I am working on this and will let you know when I have more info.

Doei,
Wayne


-----Original Message-----
From: Boer, J.M. (HKG) [mailto:J.M.Boer@lumc.nl]
Sent: Thursday, February 20, 2003 5:05 PM
To: Wakeman, Wayne
Cc: Sterrenburg, E. (HKG)
Subject: RE: rosetta question (Heat3287)


Hoi Wayne,


I think I have still one questions standing out with you: the
differentiation of flagging. We want to keep the spots that GenePix flags
automatically, because they mostly represent genes that are low/not
expressed in that particular sample (which is informative). We also flag by
hand the spots we don't trust because of background and other artifacts.
These we really want to exclude from the analysis. They get different codes,
-100 (self) and -50 (GenePix). In Rosetta there is only one type: true or
false. Can there be more?

Kind regards,
Judith
[reply to this message]

[new message]
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
Re: Hainofaft
Ivo Fokkema
2011-01-17 11:30:46