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Re: Heat 4789:Spots with no signal
Ellen Sterrenburg <E.sterrenburg@lumc.nl>
2003-07-14 15:04:57
Hi Wayne,

In the trend viewer under 'Groups' and then 'Define Signature' there are
already several options.
It would be nice if in this window you can also choose for: Signal > BG +
2SD in at least 1 Experiment.
In the .gpr (Genepix) files that we load, there is already a colum with
information about this.
It is the " % > B1+2SD " colum, which gives the percentage of pixels in a
spot that has more signal than the background plus 2 standard deviations
(SD).
I hope this can help you to find a solution.

Best regards, Ellen

Hi Ellen

I was actually just going over an idea that a colleague had for your
question. His message is below. It is kind of a long workaround depending
on how many experiments are in the trend but it should give you the answer
you are looking for.

Unfortunately, the " % > B1+2SD " column from the GenePix file is not parsed
into Resolver because GenePix is the only Technology Type that uses it. I
will enter a feature request for some way to filter on intensity.

Have a look at the strategy below and let me know if it is practical for you
or not.

Best regards,
Wayne

**********************************************************************
Here's what I found out in 3.2.2: the filter options still aren't good
enough to do what she's asking here--we get log(ratio), log(error), and
p-value. log(error) might give her an alternate way to get where she wants
to be, but maybe not.

But there is a workaround that isn't too odious for a smallish number of
experiments (say 10 or less).

1) Open the trend
2) Open one of the experiments which contributes to the trend. Go to
Groups->Filter and define the filter as you want it (probably "Intensity 1
less than X" or "Intensity 2 less than X").
3) Close the experiment. This saves your preferences, including the filter
settings.
4) Individually open all of the experiments which contributed to the trend.
5) Windows->Tile Windows (not technically necessary, but it makes the next
steps easier).
6) In the first individual experiment window, do Edit->Select Visible
followed by Edit->Broadcast Selection.
7) In the rest of the individual experiment windows, do
, - Groups->Selection->Hide other
, - Edit->Clear Selection
, - Edit->Select Visible
, - Edit->Broadcast selection
8) In the trend window, do Groups->Selection->Hide Others.

That will leave you with the sequences which meet the trend signature
criteria AND which are above the lower intensity cutoff in EVERY experiment.

This sounds complicated, but I ran through it for a 5 experiment trend in
about a minute.

Hi Wayne,

Thanks for the quick answer!
It does work the way your colleague described but I want to select genes even if there is only signal in one experiment (a gene can have no expression at one timepoint and a significant expression at another timepoint). But I think I can make a bioset for this (I'll try).
And also the way of selecting on intensity is a bit subjective. Each array is different and when I select on all spots that have an intensity > 0.2 (for instance), this can include more spots in one array in comparison with another.
However, I will work with this option for now, but it would be nice if in the future a more general algoritm is available to select for spots that have no signal.

Best regards,

Ellen

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[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