Activity for Jeff Howbert
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Jeff Howbert posted a comment on ticket #305
Hi Kaipo, The new formula you propose is correct. Jeff On Fri, 21 Aug 2015, Kaipo...
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The S and Z lines in Bill's example do not agree. As a reminder, the mass on the...
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test of svn commit
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test of commit
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I compiled the current Crux trunk, and ran the command line I posted when I originally...
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Hi Kaipo, When I set --original-output=T, it gets rid of all the nonsense columns...
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I applied Kaipo's updated version of the patch (from 2015-05-13) to a fresh copy...
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I applied Kaipo's updated version of the patch (from 2015-05-13) to a fresh copy...
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Hi Kaipo, I think we should leave #224 open until we know that addressing #221 actually...
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I reinvestigated this Issue using a Linux binary (not Windows) built from trunk on...
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I have revisited the original problem in this Issue, i.e. the --feature-in-file command...
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When I use Percolator with exact p-values, I convert to -log10(p-value) first. I...
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search-for-xlinks fails to generate q-values
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fixed problem with column header name in xhhc_s...
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Hi Sean, Some more information ... The column header in search-for-xlinks.decoy.txt...
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Hi Sean, When I applied the patch it changed the name of the column header in search-for-xlinks.target.txt,...
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Hi Sean, I don't see an attachment. Do I need to look on SourceForge? Thanks. Jeff...
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search-for-xlinks fails to generate q-values
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Hi ALice, Your proposed fix for the first formula looks correct. Please implement....
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Hi Bill, Kaipo, I looked at Bill's plots, and I don't see any obvious problem with...
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Hi Kaipo, I did further testing and it turns out I was mistaken about the file extension...
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strange behavior of Crux Percolator in Windows
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Percolator command line option not valid in Windows binary
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I could swear I fixed that a couple of months ago. I'll check, but could you also...
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lys-C gave trypsin-like digestion?
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Hi Kaipo, Ah ... I wasn't looking at the Comet or Mascot documentation. The online...
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lys-C gave trypsin-like digestion?
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tide-index and tide-search usage notes do not show all defaults
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Hi Kaipo, I didn't we write that code, so I can't comment on the importance of any...
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expanded comments on exact-p-value parameter in...
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FWIW, that weird format is lowercase hexadecimal scientific notation; see http://www.cplusplus.com/reference/cstdio/printf/...
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changed deltaMassCol from array to vector in Ti...
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changed deltaMassCol from array to vector in Ti...
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commit back to trunk of merge from crux-pvalues...
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Merge from trunk into crux-pvalue branch
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fix calculation of deltaCn with XCorr p-values
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This is addressed by the merge of the crux-pvalue branch into trunk (for non-terminal...
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This is addressed by the merge of the crux-pvalue branch back into trunk. This issue...
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This is addressed by the merge of the crux-pvalue branch back into trunk.
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commit to crux-pvalue branch after merge from t...
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Copy of trunk rev 16507 to create new branch cr...
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removed PinXMLWriter.cpp/.h
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commit of merge from crux trunk (rev 16497) int...
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commit of merge from crux trunk (rev 16491) int...
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After looking at the parameter file I had the same suspicions as Attila. He is correct....
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after testing for correct function of static N-...
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Make p-values work with different enzymes
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things to add, improve, or otherwise address in XCorr p-value code
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For DIA data I think you want the isolation window written the S line. Maybe this...
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fixed bug in access of evidence vector by N-ter...
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1) enabled support for arbitrary non-terminal s...
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after merge from trunk
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Further improvements to FAQ #3.
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Add an FAQ entry describing how the m/z axis is discretized in tide and comet
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Cleaned up numerous details in FAQ #3, and added FAQ #4 on how binned masses are...
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Cleaned up numerous details in FAQ #3, and adde...
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bad smoke test input file
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xlink.ms2 has been replaced with a new version which has correct S and Z line ma...
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Replaced xlink.ms2 with a new version in which ...
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1) Fixed bug in SpectrumRecordWriter.cpp that c...
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I have reproduced the seg fault in the standalone version of the p-value code by...
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For this change to have the full desired benefit on performance, it will be necessary...
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I've been through the p-value code, and I have a rough idea of where the problems...
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OK, consider it officially code-reviewed and approved. Thanks for fixing it.
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How does it work from here? Will you (Sean) commit the patched version?
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That works perfectly on the particular set of 10 dta files I wanted to convert. I...
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The Z line mass in the ms2 file doesn't quite agree with the M+H mass in dta (off...
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Hi Sean, I didn't receive any attachment. ??? Jeff On Mon, 13 Jan 2014, sjoemac wrote:...
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bad smoke test input file
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dta2ms2.py needs fixing
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In tide/spectrum_preprocess2.cc, function ObservedPeakSet::PreprocessSpectrum, fragment...
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Regarding removal of fragment peaks in the vicinity of the precursor m/z ... Crux's...
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Some history on 10-bin normalization of the observed spectrum in createIntensityArrayObserved()...
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major update, with working integration of XCorr...
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