User: Thomas Lin Pedersen

Reputation:
70
Status:
Trusted
Location:
Copenhagen, Denmark
Website:
https://github.com/tho...
Last seen:
3 years, 4 months ago
Joined:
6 years, 1 month ago
Email:
t********@gmail.com

I'm a PhD student at Center for Biological Sequencing, Technical University of Denmark and Chr. Hansen A/S. My main interests are analysis of proteomic data as well as visualisation of biological data in general. I believe engaging and intuitive interfaces to the increasingly complex biological data that gets generated are paramount to innovation within the area.

Posts by Thomas Lin Pedersen

<prev • 16 results • page 1 of 2 • next >
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Comment: C: XCMS for targeted metabolomic/lipidomics/proteomics
... To be honest, no. Partly because I won't have time to be your private R helpdesk, but most importantly because our correspondence would not benefit others. Please pose your questions here, on Stack Overflow, or file issues on GitHub, so that others with the same questions can learn from them... ...
written 3.4 years ago by Thomas Lin Pedersen70
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Answer: A: XCMS for targeted metabolomic/lipidomics/proteomics
... In principle yes. The big issue here is the poor connection between derived and raw data within the xcms framework (i.e. how to link MS2 scans to detected peaks etc.). My first stab at solving this is a rather convoluted and horrible package (it was my first R package) called pepmaps (https://github ...
written 3.4 years ago by Thomas Lin Pedersen70
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Comment: C: MSGFgui tries to locate MSGF.zip from a nonexistent UCSC source
... I see your point, but I would argue (probably badly) that this type of package would always be user installed - i.e. located a place where the user has write access. I very much prefer to have all package related files in one place ...
written 3.5 years ago by Thomas Lin Pedersen70
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Answer: A: MSGFgui tries to locate MSGF.zip from a nonexistent UCSC source
... It seems that the MSGF+ source has been moved (though Sangtae Kim promised me it would be a safe link - he probably forgot :-). While I cook up an official workaround you should be able to bypass this by moving your own MSGFPlus.jar file into the location given by this R command: file.path(system. ...
written 3.5 years ago by Thomas Lin Pedersen70
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Comment: C: R crashes when computing score on data from mzIdentML file
... Just to clear out, you have access to exactly the same information using mzID as mzR, so if it is critical for you you can still use mzID though the method to get scores will be different... Best Thomas > Den 16/07/2015 kl. 09.45 skrev Diego Diez [bioc] <noreply@bioconductor.org>: > & ...
written 3.9 years ago by Thomas Lin Pedersen70
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Answer: A: Difference between methods getEIC and rawEIC for xcmsRaw classes
... From the xcms documentation: "(rawEIC) Generate extracted ion chromatogram for m/z values of interest. The raw data is used in contrast to getEIC which uses data from the profile matrix." rawEIC ignores any binning done and reads the raw data, while getEIC is based on the binned data... best Tho ...
written 4.1 years ago by Thomas Lin Pedersen70
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Comment: C: Unexpected total ion count (TIC) with xcms package
... As I said, yes, these values represent the true unprocessed total ion count as reported by the instruments, thus before any processing of the spectra is done. As to what to use it depends - If you've done serious changes to the spectra I would recalculate. Otherwise the differences between the two a ...
written 4.1 years ago by Thomas Lin Pedersen70
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Comment: C: Unexpected total ion count (TIC) with xcms package
... But only if the tic slot of Tour xcmsRaw object is empty, which it shouldn't be in case of mzML/mzXML (again - never used netCDF so wouldn't know about that) - have you checked the content of the tic slot? ...
written 4.1 years ago by Thomas Lin Pedersen70
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Comment: C: Unexpected total ion count (TIC) with xcms package
... Out of curiosity - what c-code? plotTIC is pure R and all internal parsing of raw data is handled by mzR... ...
written 4.1 years ago by Thomas Lin Pedersen70
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Comment: C: Unexpected total ion count (TIC) with xcms package
... Just had a look at the source and it is indeed reading hard coded values if they are present - you can check if these values are there by looking at object@tic. If your object have content in the tic slot then thats the answer to your question... ...
written 4.1 years ago by Thomas Lin Pedersen70

Latest awards to Thomas Lin Pedersen

Scholar 4.1 years ago, created an answer that has been accepted. For A: How to get from xcmsRaw to a xcmsSet
Scholar 4.2 years ago, created an answer that has been accepted. For A: How to get from xcmsRaw to a xcmsSet
Autobiographer 4.7 years ago, has more than 80 characters in the information field of the user's profile.

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