From: Larson, T. <tr...@yo...> - 2008-10-17 11:25:16
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Dear Chris, Thanks for the quick reply - that was exactly the information I needed. I will run some tests. I have one more question. Is there an easy way to batch signal processing for several files? I'm talking hundreds of files here, and I don't want tot do them one by one. I have run batches using Windows command line with reAdW for converting thermo .raw to .mzXML format using for-in-do syntax. This works because reAdW only needs the source file and converts to the output format with no other user input needed. I assume this won't work for the openms tools because an -out filename needs to be explicitly specified for each file? Is there a way to automatically specify an output name to a file while batching - e.g. to append "filtered" to the input file "test.mzData" so that it is automatically renamed to "test_filtered.mzData" during a batch execution of baselineFilter? thanks Tony thnaks Tony - however, this Chris Bielow wrote: > Hi Tony, > > Larson, TR wrote: >> Hello, >> I am completely new to using openms; yesterday I downloaded openms 1.2 >> to have a play around with it. My primary interest is in processing and >> peak-picking from LCMS and GCMS .cdf data files. I was initially pointed >> to openms from users of the R package, xcms, because I needed to find a >> tool to pre-process my .cdf files; specifically to remove noise from the >> chromatograms before further processing. >> >> openms is the only package I found that can do this with .cdf files. >> I've managed to work out how to use BaselineFilter, FileFilter, and >> FileConverter from the TOPP command line interface. >> >> What I am typically doing is using FileConverter to get my .cdf files >> into .mzData format, then applying BaselineFilter to reduce the baseline >> noise, and finally using FileFilter to remove the residual noise below >> an intensity threshold. >> >> However, I'm confused because the Signal Processing tutorial in the >> openms .html documentation lists gaussian and savitzy-golay smoothing >> filters in addition to the baseline filter - but I can't find either of >> these from the TOPP command line. > > Have a look at NoiseFilter.exe > which has a -type parameter: > > Options (mandatory options marked with '*'): > -in <file>* Input raw data file (valid formats: 'mzData') > -out <file>* Output raw data file (valid formats: 'mzData') > -type <type>* Smoothing filter type (valid: 'sgolay,gaussian') > > > >> I'm also interested in other signal >> noise processing, such as per-spectra thresholding, but there doesn't >> seem to be a tool in openms for this. > > You could for example use FileFilter.exe with its -sn <number> Option. > <number> is the minimal Signal-To-Noise ratio a peak needs to have in order to > pass the filter. It works scanwise. > Use '1' to filter about 50% of the data (as the noise is estimated using the > median of a sliding window). Higher numbers will filter out more peaks (with > e.g. '10' being very aggressive), lower SN values will filter out fewer peaks. > Play with it a little until you find the settings which fit your needs. > >> I'm not a programmer, but I do want to make best use of openms. Can >> someone please help me to understand how to apply these other signal >> processing techniques to my data? Is this possible from the TOPP >> command line using one of the .exe files or must I do it another way? >> I've looked through all the documentation and I can't work it out. > > I hope the above will get you started. There is also the possibility to resample > your data using Resampler.exe to make the peaks equidistant, but that is only > needed in special cases. > > If you have more questions, don´t hesitate to ask :) > > cheers > Chris > > >> thanks >> Tony >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >> Build the coolest Linux based applications with Moblin SDK & win great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Open-ms-general mailing list >> Ope...@li... >> https://lists.sourceforge.net/lists/listinfo/open-ms-general > -- *************************************** Dr. Tony R. Larson CNAP Department of Biology, Area 7 University of York PO Box 373 York YO10 5YW UK Tel: +44(0)1904 328 826 (office) Tel: +44(0)7920 474 828 (mobile) Fax: +44(0)1904 328 762 E-mail: tr...@yo... *************************************** Disclaimer: This email and any attachment(s) are strictly confidential and contain information intended only for the use of the individual(s) named above. If you are not the intended recipients please delete this message from your system, do not use or disclose the information in any way and notify us by return e-mail. |