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Heat 3287: flags in GenePix -> fail codes in Rosetta
Judith Boer <>
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.


-----Original Message-----
From: Boer, J.M. (HKG) []
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,
[reply to this message]

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Heat 3287: flags in GenePix -> fail codes in Rosetta
Judith Boer
2003-03-03 12:04:44
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Judith Boer
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cell number
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2009-01-13 21:07:52
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Ivo Fokkema
2011-01-17 11:30:46