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