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Combine-on-the-fly of experiments no longer possible
Peter-Bram 't Hoen <p.a.c.hoen@lumc.nl>
2005-04-13 10:21:54
The COTF at the Ratio Experiment level did not take into account multiplicative error when starting from the Ratio Expt view. During the "Squeeze Ratios" operation in the pipeline, which squeezes Reporter-level to Sequence-level, an error-flooring step is applied. However, multiplicative error is not available for Ratio Experiments when Combined on-the-fly (but available in ED combine and in COTF starting from Ratio Profile view), so it used the default error floor and adjusted all error values below 0.1 to 0.1, resulting in the apparent discrepancies when compared to data from the ED. COTF was really meant to be a "quick and dirty" way to see how experiments might look if you combine them. When you select profiles or experiments for COTF, the engine only goes back as far as it needs to get data to combine. It was a feature back when a profile could only participate in one experiment in the Resolver database, and existing experiments would have to be broken up if you wanted a profile to be combined into a different experiment. So a user could use COTF to quickly see if it would be worth combining two experiments. However, now if you want to see how profiles or experiments would look combined together, you can build a new ED and simply delete it if you don't like it. For this reason we decided to delete the COTF at the RE level.

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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
Re: Hainofaft
Ivo Fokkema
2011-01-17 11:30:46