Comments (20)
Hey Ethan, i was actually not aware of that, that sounds excellent! I will try it and upload the ascii file for you.
Thanks again,
Silas
from chromconverter.
Hey Ethan, here is the corresponding ASCII from LabSolutions.
Anthocyanin_2_MeOH001.txt
from chromconverter.
Yep, you're right, i had restarted the session before reinstalling from github but didn't think to do so after... works now!
from chromconverter.
I will try to look into it, though I can't really make any promises or give you a timeline. It's a little bit tricky since the format is not documented at all, as far as I know. It would be helpful if you could provide a little more information about your file (e.g. what kind of instrument/software it was produced with and what the detectors are on the machine). Thank you for sharing the file!
Ethan
from chromconverter.
Hey Ethan, that is all i can ask! The file comes from Shimadzu Lab Solutions v 5.71. The instrument is a shimadzu LC-20 with PDA iirc, but i will double check and let you know.
from chromconverter.
Thanks. Also, you may already know this (and I know it's not as convenient as reading the .lcd
files directly), but I believe you can export the raw PDA data from LabSolutions by right clicking the sample name and selecting File Conversion:Convert to ASCII
. These ascii txt files do have a parser in chromConverter already.
Also, if you can generate the ascii file for the .lcd
file you sent it would be helpful to have as a point of comparison.
from chromconverter.
Thanks for providing this file! I don't know if you tried to read it yet using chromConverter, but it actually throws an error because it has commas as the decimal separator (european style) rather than periods (american style). I will put up a patch shortly that can read the european-style files.
from chromconverter.
This should be fixed by 725ddff. You should now be able to read in these ascii files at least:
x<-read_chroms(path_to_file_or_files, format_in="shimadzu_dad")
from chromconverter.
Hey Ethan, yep i did try it with the ascii and got an error, but didnt have time to figure out what it was about. Well, you fixed it before i even got that far so thanks once again!
from chromconverter.
edit:fixed the format_in parameter, still get an error...
edit:tried updating from CRAN and github, same thing
Warning in read_chroms(paths = "Anthocyanin_2_MeOH001.txt", format_in = "shimadzu_dad") :
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
scan() expected 'a real', got '0,00000'
I feel i should apologize on behalf of european PCs, for some reason comma is default decimal here even though it means we have to jump through all sorts of hoops with our data files...
from chromconverter.
This is the old error -- it should be fixed in the latest version. Did you refresh your R session after reinstalling the package? Usually the old package is still cached if you install a new version of a package and don't reset your R session. The CRAN version will not be updated for a while, so that one will not work.
I'd suggest:
- install new version from github:
remotes::install_github("ethanbass/chromConverter"
- Reset R session (In R studio, you can do this by selecting
Session:Restart R
). - Reload the package:
library(chromConverter)
- Try again:
read_chroms("Anthocyanin_2_MeOH001.txt", format_in="shimadzu_dad")
from chromconverter.
Excellent! I'm glad to hear it is working now
from chromconverter.
Fully willing to do what I can to help with adding a .lcd parser, it would make life a lot easier! Let me know if there is anything I can do to help.
from chromconverter.
Hi @captainsailboat. Do you need a parser for the DAD format or mass spec data? I think there are similarities but the formats aren't exactly the same. I have been working a little bit on the DAD file I got from @silasmellor and have managed to partially decode it but there are still some things I haven't been able to figure out. Do you have any experience decoding binary files? If so, I could try to share with you what I have so far and you could have a look for yourself. Otherwise, it would be helpful to have a few more example .lcd files (along with the corresponding ASCII files) to check the validity of what I've worked out so far.
from chromconverter.
I think I have this mostly figured out. I uploaded the parser to the Shimadzu LCD branch (https://github.com/ethanbass/chromConverter/tree/shimadzu_lcd) if ya'll want to try it out. I haven't figured out yet where the retention times are stored yet in the file but the absorbance values are correct (at least for the file I received from @silasmellor). It is also quite slow, it takes over a minute on my computer to parse one file. You can access the parser (for now) using the read_shimadzu_lcd
function.
from chromconverter.
I believe the final retention time should be stored somewhere in these two streams, but I haven't been able to figure out yet how it's encoded.
3D_data_item.txt
2D_data_item_stream.txt
from chromconverter.
I am struggling to figure out how to utilize this. I have installed R-studio and opened the R file, but am not sure how to actually carry out the conversion. I am also solely using this to analyze the m/z values of fragments at this time so retention times are of little interest to me. If there are instructions somewhere on how to use this script please do guide me to that location. Thank you!
from chromconverter.
Hi @captainsailboat, sorry for the misunderstanding -- the parser i've written so far can only extract the diode array detector stream as I mentioned above, which was the subject of the original issue.
I'm not sure yet how similar the encoding is for the mass spec data. While i'd be interested in trying to figure out the mass spec stream, I have very limited time to work on this and I also don't have a lot of example files to work with.
You might want to check out ProteoWizard (https://proteowizard.sourceforge.io/doc_users.html), I think they support conversions of (some?) .lcd files to mz(X)ML.
from chromconverter.
from chromconverter.
That would be helpful if you could send some example files! You should be able to upload them directly here (you may need to change the extensions to something github likes like .txt) or you could email them to me. Could you also describe in a little more detail what kind of data is contained in the two mzXML files and what form you're trying to get the data into for further analysis? If it's a similar instrument to the one discussed in this thread (rietho/IPO#32) it sounds like maybe the two files contain data from positive and negative ionization modes...?
Ethan
from chromconverter.
Related Issues (19)
- Interface to OpenChrom file parsers HOT 1
- Path problems with system calls on Windows HOT 30
- package fails to load if python dependencies can't be installed on Windows HOT 17
- Python environment sometimes fails to load on Windows due to dependency issues
- Update chemstation 181 parser to read older FID files HOT 1
- Add R-based parser for Chemstation UV files HOT 1
- read_chroms() can't find openChrom executable HOT 4
- Python bindings don't work correctly in latest version of RStudio without altering Python settings (ModuleNotFoundError)
- Path interpretation issue in read_chroms HOT 8
- Add support for Waters PDA files HOT 1
- Issue reading in ChemStation .ch files HOT 2
- seeking chemstation version 181 file
- importing cdf (raw) from Waters HOT 8
- Chromatograms from mzXML files HOT 3
- Reading Intensities Correctly HOT 6
- Converting .cdf to .mzml - different parsers? HOT 1
- Weird error when trying to convert to cdf HOT 3
- Reading shimadzu .lcd files HOT 8
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from chromconverter.