Etchevers:Notebook/STRA6 in eye development/2009/07/30

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FindPeaks update and questions

Anthony has sent the following messages for each update to FP4 from which I've extracted what I think relevant to us:


 * Bugfix: only write out filtered peaks if not (index == -1). (e.g. there is a peak there.)
 * Bugfix: Retrieving control threshold fails when dataset is empty. Now returns a threshold of zero. (Bug identified by Deniz Koellhofer)
 * ApplyCompare can now write out a wig for just filtered peaks.


  * Nothing special for us.


 Version 4.0.3 provides bug fixes for several advanced features including a more appropriate window size for 
 * peak pairing in compare/control mode,  
 * fixes incorrect pairing of chromosomes under certain conditions for control/compare, 
 * fixing correct minimum height when writing out files.
 This version also now adds the ability to provide jpg/png graphics of the compare/control results being processed.
 * Bugfix: Incorrect variable while writing out mapfiles.
 * A simple library for producing graphs within the context of FindPeaks.  Supports PNG and JPG.
 * Replacing the overly specific variable pair object with a more generic model: Tuple<Object,Object>
 * Upgrade all FindPeaks Modules to use Tuple<> instead of IntPair, FloatPair, FloatInt objects.
 * Update Build.xml to include Tuple.class
 * First Pass build of HistogramImage creating object.  Will take any histogram and generate a histogram image.
 * minor improvements to image libraries.
 * Adding SVN:Keywords to new objects
 * Bugfix: writing out files was dropping the minimum height requirement due to the incorrect use of a gt or eq, instead of just gt 
 * Bugfix: applycontrol parameters should be sent the whole dataset, which will require normalizing for proper statistics.
 * LinearRegressionPerpendicular now exposes slope for use in higher up normalizations.
 * Apply Control now requires a normalization for significance calculation.  This replaces the previous method of 
 * calculating p-values for the peaks in the peak files (when available.) 
 * FindPeaks now makes appropriate calls to get Normalization factor and utilize it (when available) for writing out peaks files. 
 * PeakDataSetParent uses normalization and passes it along to write out peaks files.
 * Change default window_size to 400.  100 was WAY too small. [We used first the default 100 then tried 50]
 * Significantly upgraded the graphics produced by graphimage. Applycompare now uses them.
 * Update build.xml to include graphic generating files used for compare scatterplots.
 * Added ability to generate lines to graph image  (based on slope and intercept)
 * ApplyCompare now also writes lines to image 
 * Producing two jpgs: before and after filtering, for greater clarity.
 * Flip height and width in basic image init, to conform with the rest of the graphics package standard notation.
 * New Error checking on AlignedRead direction.  Must be "+" or "-"

So it looks like we should install version 4.0.3 (possibly here?)

Will want to ask why .wig files are so bloody enormous that we have to upload them to UCSC from a server to be efficient, and why UCSC only takes five? (Unpacked, they were 3.6-3.7 Gb each, just for one chromosome.) Also, once the .wig files are up, what is the unit on the y axis? We are getting between 0 and 1, which is odd.

I'm in !!!! Nicolas